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.