Why shouldn't a starship have an industrial replicator aboard? How else are they going to do repairs if they're light-years away from a starbase? It makes perfect sense that they're able to build new shuttles and torpedoes. With replicators, you can build anything as long as you have raw materials and energy. The only reason Voyager had shortages early on was because their power was limited. There are plenty of legitimate inconsistencies in Voyager, but this is not one of them.
Well, it would make perfect sense, if they hadn't said this
[from "The Cloud"
, as in the first seconds of the OP video]:
CHAKOTAY: We have a complement of thirty eight photon torpedoes at our disposal, Captain.
JANEWAY: And no way to replace them after they're gone.
If the argument is that they built their own replication system, given how urgent it was and given that they'd have plenty of time to accomplish that,
fine. But that they shipped out with the ability to make their own torpedoes at the push of a button? No way.