Shops and game design

This is probably going to be a little rambly of a post, but I'm a little stuck right now: what do I do about shops and money?

I'm not experienced at game design, so if this is a solved problem I'd like to know.  The most abstract version of this question is: what is the best way to balance finite-short-term-but-infinite long-term resources against infinite-short-term-but-finite-long-term resources?

Basically, it's about money (which is infinite in the long term), items (finite in the short term since they can only be replenished at each shop, and value ranges wildly betwqeen in-combat or out of combat), and the in-combat turn (where the time spent using an item is a costly, and very finite resource, but is unlikely to run a prepared player out of an item).

So, items range from being effectively finite out of combat where the limit is the number you will need to get to the next town, to being infinite in combat where the limit is the number you can use in a single turn.  Is it even possible to balance the items in both of these ways?

If the player plays long enough, they will have enough of all the items in the shop.  If I assume they don't, the game might be too easy for those who do.  If I assume they do, the game risks being too difficult for those who don't.  Since this is FF6, is it preferable to err on the side of the player being overpowered?

Am I overthinking this?  I am just concerned over nothing, aren't I?