>The ship started out with 38 torpedoes and no way to replace them (stated explicitly in dialogue!) and by the end of the show they had used something like 85 of them.

I get where you're coming from, and they definitely would have been better served to a) not say that, or b) resolve it at some later time. That said, part of what made Voyager interesting (to me) was that they had basically taken house cats and thrown them into the wild. In Federation space there was never a need or desire to make new photon torpedoes on the fly, but in the Delta quadrant for seven years they probably figure something out.