Map editing: List of unused tilemaps?

I don't know the inner workings of FF6LE-CE very well, but I think I can answer your questions in general.

1) Here's a list of all the tilemaps that show up in the vanilla maps (sorry the indices are in decimal, not hex). If it's not in the list, it's never used. I think you got all of them. You can also use tilemap 0x0144. I think you should be able to use any of the unused ones with no problems.

Code:

0: None
1: Kohlingen: Exterior (BG1)
2: Kohlingen: Exterior (BG2)
3: Mobliz: Exterior (BG1)
4: Mobliz: Exterior (BG2)
5: Thamasa: Exterior (BG1)
6: Thamasa: Exterior (BG2)
7: South Figaro: Exterior (BG1)
8: South Figaro: Exterior (BG2)
9: Doma Castle: Exterior (BG1)
10: Doma Castle: Exterior (BG2)
11: Figaro Castle: Exterior (BG1)
12: Figaro Castle: Exterior (BG2)
13: Albrook: Exterior (BG1)
14: Albrook: Exterior (BG2)
15: Albrook: Docks (BG1)
16: Albrook: Docks (BG2)
17: Kohlingen: Interior (BG1)
18: Kohlingen: Interior (BG2)
19: Figaro Castle: Interior (BG1)
20: Figaro Castle: Interior (BG2)
21: Sabin's House: Exterior (BG1)
22: Sabin's House: Exterior (BG2)
23: Cave to South Figaro (BG1)
24: Cave to South Figaro (BG2)
25: Lete River: Exterior (BG1)
26: Lete River: Exterior (BG2)
27: Lete River: Exterior (BG3)
28: Imperial Camp: On Foot (BG1)
29: Imperial Camp: On Foot (BG2)
30: Vector: Castle Interior (BG1)
31: Vector: Castle Interior (BG2)
32: South Figaro: Interior (BG1)
33: South Figaro: Interior (BG2)
34: Nikeah: Exterior (BG1)
35: Nikeah: Exterior (BG2)
36: Cutscene (BG1)
37: Cutscene (BG2)
38: Cave to the Sealed Gate (BG1)
39: Cave to the Sealed Gate (BG2)
40: Umaro's Cave (BG1)
41: Umaro's Cave (BG2)
42: Mt. Kolts: Exterior (BG1)
43: Mountains Parallax (BG2)
45: Mt. Kolts: Interior (BG1)
46: Mt. Kolts: Interior (BG2)
47: Mt. Kolts: Interior (BG3)
48: Solitary Island: Cliff (BG1)
49: Solitary Island: Cliff (BG2)
50: Albrook: Interior (BG1)
51: Albrook: Interior (BG2)
52: Nikeah: Interior (BG1)
53: Nikeah: Interior (BG2)
54: Narshe: South Exterior (BG1)
55: Narshe: South Exterior (BG2)
56: Maranda: Exterior (BG1)
57: Maranda: Exterior (BG2)
58: Phoenix Cave: Upstairs (BG1)
59: Phoenix Cave: Upstairs (BG2)
60: South Figaro: Docks (BG1)
61: South Figaro: Docks (BG2)
62: Narshe: Hills Maze (BG1)
63: Narshe: Hills Maze (BG2)
64: Phantom Train: Front Cars (BG1)
65: Phantom Train: Seating Cars (BG1)
66: Phantom Train: Seating Cars (BG2)
67: Phantom Train: Caboose Room and Engine Room (BG1)
68: Phantom Train: Caboose Room and Engine Room (BG2)
69: South Figaro: Basement (BG1)
70: South Figaro: Basement (BG2)
71: Phantom Train: Dining Car (BG1)
72: Phantom Train: Dining Car (BG2)
73: Phantom Train: Rear Cars (BG1)
74: Fanatics' Tower: Bottom (BG1)
75: Phantom Train: Seating Car with Switch (BG1)
76: Phantom Train: Seating Car with Switch (BG2)
77: Fanatics' Tower: Bottom (BG2)
78: Thamasa: Burning Building (BG1)
79: Phantom Train: Hallway (BG1)
80: Phantom Train: Hallway (BG2)
81: Phantom Train: Caboose (BG1)
82: Phantom Train: Caboose (BG2)
83: Zozo: Exterior (BG1)
84: Zozo: Exterior (BG2)
85: Vector: Town Exterior (BG1)
86: Vector: Town Exterior (BG2)
87: Figaro Castle: Basement (BG1)
88: Figaro Castle: Basement (BG2)
89: Returner's Hideout (BG1)
90: Returner's Hideout (BG2)
91: Phantom Train: Small Rooms (BG1)
92: Phantom Train: Small Rooms (BG2)
93: Mobliz: Interior (BG1)
94: Mobliz: Interior (BG2)
95: Thamasa: Interior (BG1)
96: Thamasa: Interior (BG2)
97: Zozo: Exterior (BG3)
98: Big Fog Parallax (BG3)
99: Floating Island: Exterior (BG1)
100: World Parallax (BG2)
101: Vector: Town On Fire (BG1)
102: Vector: Town On Fire (BG2)
103: Opera House: Theater (BG1)
104: Opera House: Theater (BG2)
105: Figaro Castle: Submerging (BG1)
106: Figaro Castle: Submerging (BG2)
107: Narshe: Cliffs (BG1)
108: Narshe Parallax (BG2)
109: Narshe: Mountaintop (BG1)
110: Cyan's Dream: Caves (BG2)
111: Narshe: Interior (BG1)
112: Narshe: Interior (BG2)
113: Narshe: North Exterior (BG1)
114: Narshe: North Exterior (BG2)
115: Magitek Factory: Other Rooms (BG1)
116: Magitek Factory: Other Rooms (BG2)
117: Zozo: Interior (BG1)
118: Zozo: Interior (BG2)
119: Doma Castle: Interior (BG1)
120: Doma Castle: Interior (BG2)
121: Jidoor: Exterior (BG1)
122: Jidoor: Exterior (BG2)
123: Jidoor: Interior (BG1)
124: Jidoor: Interior (BG2)
125: Narshe: North Caves (BG1)
126: Narshe: North Caves (BG2)
127: Cyan's Dream: Cliffs (BG1)
128: Cyan's Dream: Cliffs (BG2)
129: Mobliz: WoR Exterior (BG1)
130: Mobliz: WoR Exterior (BG2)
131: Cyan's Dream: Caves (BG3)
132: Cyan's Dream: 3rd Train Car (BG1)
133: Vector: Town Interior (BG1)
134: Vector: Town Interior (BG2)
135: Imperial Base: Exterior (BG1)
136: Imperial Base: Exterior (BG2)
137: Esper World: Exterior (BG1)
138: Esper World: Exterior (BG2)
139: Esper Mountain: Exterior B (BG1)
140: Vector: Town On Fire (BG3)
141: Mt. Zozo: Bridge (BG1)
142: Gogo's Room (BG1)
143: Esper Mountain: Exterior C (BG1)
144: Cyan's Dream: Caves (BG1)
145: Mt. Zozo: Cliff to Cyan's Cave (BG1)
146: Gogo's Room (BG2)
147: Mt. Kolts: Vargas' Area (BG1)
148: Mt. Kolts: Vargas' Area (BG2)
149: Esper Mountain: Statue Cave/Exterior A (BG1)
150: Esper Mountain: Statue Cave/Exterior A (BG2)
151: Mt. Zozo: Treasure Cliff (BG1)
152: Mt. Zozo: Treasure Cliff (BG2)
153: Narshe: South Caves (BG1)
154: Narshe: South Caves (BG2)
155: Phantom Train: Torches Parallax (BG2)
156: Phantom Train: Platform (BG2)
157: Narshe: South Exterior (BG3)
158: Narshe: North Caves (BG3)
159: Figaro Castle: Empty Desert (BG1)
160: Cave to South Figaro (BG3)
161: Magitek Factory: Upper Room (BG1)
162: Magitek Factory: Upper Room (BG2)
163: Crescent Mountain: Exterior (BG1)
164: Crescent Mountain: Exterior (BG2)
165: Crescent Mountain: Exterior (BG3)
166: Crazy Old Man's House: Exterior (BG1)
167: Crazy Old Man's House: Exterior (BG2)
168: Crazy Old Man's House: Interior (BG1)
169: Crazy Old Man's House: Interior (BG2)
170: Baren Falls: Interior (BG1)
171: Baren Falls: Interior (BG2)
172: Mountaintop (BG1)
173: Waterfall Parallax (BG2)
174: Baren Falls: Interior (BG3)
175: Esper World: Interior (BG1)
176: Esper World: Interior (BG2)
177: Esper World: Interior (BG3)
178: Thamasa: Burning Building (BG2)
179: Riverbank (BG1)
180: Riverbank (BG2)
181: Darill's Tomb: Entrance (BG1)
182: Darill's Tomb: Entrance (BG2)
183: Airship: Interior (BG1)
184: Airship: Interior (BG2)
185: Blackjack: Exterior (BG1)
186: Clouds Parallax (BG2)
187: Falcon: Exterior (BG1)
188: Cyan's Dream: 2nd Train Car (BG1)
189: Cyan's Dream: 2nd Train Car (BG2)
190: Narshe: North Exterior (BG3)
191: Cyan's Dream: 3 Stooges (BG1)
192: Nikeah: Docks (BG1)
193: Nikeah: Docks (BG2)
194: Crescent Mountain: Interior (BG1)
195: Crescent Mountain: Interior (BG2)
196: Baren Falls: Entrance (BG1)
197: Baren Falls: Entrance (BG2)
198: Phantom Forest: Main Area (BG1)
199: Forest Parallax (BG2)
200: Forest Parallax (BG3)
201: Vector: Lower Castle Exterior (BG1)
202: Vector: Lower Castle Exterior (BG2)
203: Vector: Upper Castle Exterior (BG1)
204: Vector: Upper Castle Exterior (BG2)
205: Solitary Island: Beach (BG1)
206: Solitary Island: Beach (BG2)
207: Solitary Island: Beach (BG3)
208: Solitary Island: House Exterior (BG1)
209: Solitary Island: House Exterior (BG2)
210: Magitek Research Facility: Esper Room (BG1)
211: Magitek Research Facility: Esper Room (BG2)
212: Phantom Train: Forest Parallax (BG2)
213: Colosseum Guy's House: Exterior (BG1)
214: Colosseum Guy's House: Exterior (BG2)
215: Magitek Factory: Lower Room (BG1)
216: Magitek Factory: Lower Room (BG2)
217: Cave to the Sealed Gate: Gate (BG1)
218: Cave to the Sealed Gate: Gate (BG2)
219: Imperial Camp: Magitek Armor (BG1)
220: Imperial Camp: Magitek Armor (BG2)
221: Kohlingen: Exterior (BG3)
222: Narshe: Cliffs (BG3)
223: Returner's Hideout (BG3)
224: Thamasa: Burning Building (BG3)
225: Phantom Forest: Recovery Spring (BG1)
226: Phantom Forest: Fork (BG1)
227: Phantom Forest: Path to Phantom Train (BG1)
228: Serpent Trench: Caves (BG1)
229: Serpent Trench: Caves (BG2)
230: Serpent Trench: Caves (BG3)
231: Opera House: Sky Parallax (BG2)
232: Opera House: Castle (BG1)
233: Tzen: Exterior (BG1)
234: Tzen: Exterior (BG2)
235: Narshe: South Caves (BG3)
236: Colosseum Guy's House: Exterior (BG3)
237: Darill's Tomb (BG1)
238: Darill's Tomb (BG2)
239: Darill's Tomb (BG3)
240: Esper Mountain: Caves (BG1)
241: Esper Mountain: Caves (BG2)
242: Esper Mountain: Caves (BG3)
243: Gogo's Cave (BG1)
244: Gogo's Cave (BG2)
246: Esper World: Exterior (BG3)
247: Magitek Research Facility: Tube Room (BG3)
248: Magitek Research Facility: Esper Room (BG3)
249: Esper World: Doors Closing (BG1)
250: Esper World: Doors Closing (BG3)
251: Fanatics' Tower: Exterior (BG1)
252: Fanatics' Tower: Exterior (BG2)
253: Fanatics' Tower: Top (BG1)
254: Cutscene (BG1)
255: Cutscene (BG2)
256: Magitek Research Facility: Elevator (BG1)
257: Magitek Research Facility: Elevator (BG2)
258: Jidoor: Floating Island Shadow (BG3)
259: Empty (BG1)
260: Mobliz: Exterior (BG3)
261: Cyan's Dream: 3rd Train Car (BG2)
262: Mobliz: WoR Exterior (BG3)
263: Mt. Zozo: Interior (BG1)
264: Mt. Zozo: Interior (BG2)
265: Mt. Zozo: Interior (BG3)
266: Ancient Castle: Cave (BG1)
267: Ancient Castle: Cave (BG2)
268: Ancient Castle: Interior (BG1)
269: Ancient Castle: Interior (BG2)
270: Ancient Castle: Exterior (BG1)
271: Ancient Castle: Exterior (BG2)
272: Fanatics' Tower: Top (BG2)
273: Fanatics' Tower: Treasure Room (BG1)
274: Colosseum (BG1)
275: Colosseum (BG2)
276: Darill's Tomb: Stairway (BG1)
277: Gogo's Room (BG3)
278: Cave in the Veldt (BG1)
279: Cave in the Veldt (BG2)
280: Kefka's Tower: Exterior (BG1)
281: Darill's Tomb: Stairway (BG2)
282: Kohlingen: Phoenix (BG3)
283: Phoenix Cave: Downstairs (BG1)
284: Phoenix Cave: Downstairs (BG2)
285: Thamasa: House on Fire (BG3)
286: Fanatics' Tower: Treasure Room (BG2)
287: Fanatics' Tower: Top Treasure Room (BG1)
288: Fanatics' Tower: Top Treasure Room (BG2)
289: Ebot's Rock: Teleport Caves (BG1)
290: Ebot's Rock: Teleport Caves (BG2)
291: Ebot's Rock: Other Caves (BG1)
292: Ebot's Rock: Other Caves (BG2)
293: Chocobo Stable: Exterior (BG1)
294: Chocobo Stable: Exterior (BG2)
295: Phoenix Cave: Upstairs (BG3)
296: Small Fog Parallax (BG3)
297: Kefka's Tower: Exterior (BG2)
299: Kefka's Tower: Top (BG1)
300: Kefka's Tower: Waterfall Parallax (BG2)
303: Kefka's Tower: Lower Switch Room (BG1)
304: Kefka's Tower: Lower Switch Room (BG2)
305: Gogo's Cave (BG3)
306: Lete River: Caves (BG1)
307: Lete River: Caves (BG2)
308: Lete River: Caves (BG3)
309: Kefka's Tower: Castle Rooms (BG3)
310: Kefka's Tower: Misc. Rooms (BG1)
311: Floating Island: Save Point (BG1)
312: Floating Island: Save Point (BG2)
313: Floating Island: Save Point (BG3)
314: Kefka's Tower: Misc. Rooms (BG2)
315: Kefka's Tower: Castle Rooms (BG1)
316: Kefka's Tower: Castle Rooms (BG2)
317: South Figaro: Exterior (BG3)
318: Nikeah: Exterior (BG3)
319: Albrook: Exterior (BG3)
320: Maranda: Exterior (BG3)
321: Kefka's Tower: Top Parallax (BG2)
322: Kefka's Tower: Factory Rooms (BG3)
323: Magitek Research Facility: Broken Tubes (BG3)
324: Map 333 (BG3)
325: Kefka's Tower: Top (BG2/BG3)
326: Cyan's Dream: 3 Stooges (BG2)
327: Albrook: Docks (BG3)
328: South Figaro: Docks (BG3)
329: Nikeah: Docks (BG3)
330: Waterfall Parallax (BG3)
331: Riverbank (BG3)
332: Kefka's Tower: Tube Room (BG1)
333: Kefka's Tower: Tube Room (BG2)
334: Kefka's Tower: Factory Rooms (BG1)
335: Kefka's Tower: Factory Rooms (BG2)
336: Esper Mountain: Statue Cave (BG3)
337: Kefka's Tower: Lower Switch Room (BG3)
338: Magitek Factory: Upper Room (BG3)
339: Magitek Factory: Lower Room (BG3)
340: Kefka's Tower: Ending Room (BG1)
341: Kefka's Tower: Ending Room (BG2)
342: Kefka's Tower: Ending Airship Scene (BG1)
343: Kefka's Tower: Ending Airship Scene (BG2)
344: Kefka's Tower: Ending Room (BG1)
345: Kefka's Tower: Ending Room (BG2)
346: Kefka's Tower: Ending Airship Scene (BG3)
347: Cave in the Veldt (BG3)
348: Umaro's Cave (BG3)
349: Sky Parallax (BG2)

2) I believe the upper limit for the number of tilemaps is actually 1024, because there are 10 bits available to store the index for each map.  I checked the asm code where the pointers get calculated and I didn't see anything that would overflow. I'm not sure how many FF6LE-CE supports though.

3) I think I understand what you're saying here. You should be able to use any tilemap for any layer (or multiple layers) on a map. Even layer 3, which is treated differently than layers 1 and 2 for other things.