Honestly this never bugged me >_>
We don't see EVERYTHING Voyager does. It's not unreasonable that they bought or made more torpedos on their journey in quite dull trade exchanges with friendly aliens or uneventual resource grinding on unhabbited planets.
Plusthere's the whole Goo Crew of Voyager and the show never says what epsiodes followed the goo crew and what followed the real crew. So for all we know, some of those episodes might be an entirely different ship with an entirely different compliment of torpedos.
They also never showed Harry Kim taking a dump but I don't think that means he never took one for 8 years.