They won't be infinite in the final game, surely, but after reading Linkbeck1000's post, I have something else to say.
They should have more of a limit to how the enemies keep dropping bombs and arrows and such, it seems that everywhere you go that you need some in you're always getting 10 bombs for every 3 you use. I just recently played through Ocarina of Time again and there were actually moments where I had to leave a dungeon just to buy bombs/arrows so I could beat the dungeon. It would be nice to see an actual challenge to keeping the number of your bombs/arrows up, then maybe I'd have something to spend my few thousand rupees on, unlike in TWW.