Voyager certainly wasn't the strongest of the Star Trek spin-offs, but it did have its moments. One of those moments however did not involve keeping track of exactly how many apparently non-replaceable photon torpedoes the stranded ship had. The question, then, is just how many of these powerful weapons did Voyager loose on the denizens of the Delta Quadrant?
A YouTube user by the name of "TazG2000" went through the entire series and edited together a six-and-a-half minute clip showing each instance of where one or more torpedoes were fired (or mention was made of them being fired). The audio isn't that great, but the on-screen counters that track where the photons are going is strangely comically to watch, especially when the command staff play the all-destroying "full spread" trump card.
I'm sure you could come up with some in-universe explanations for how Voyager was able to supplement her torpedo stores, though it might have been easier for the writers to ease up on the drama and not toss in Janeway's "can't be replaced" line early in the proceedings.