The dialogue in "The Cloud" doesn't read as having to do with temporary circumstances to me:
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.
You can make that rationalization to explain later episodes if you'd like, of course.
We're talking about Starfleet engineers here, with B'Elanna being an exceptionally gifted example of the breed. I find it credible that, if placed in a circumstance where they knew they had to depend on themselves with no starbase support, they would be able to innovate ways to replace things that were normally not replaceable. I mean, they'd have to, wouldn't they? There'd be no other choice.
And of course, as I said, there's the possibility of trade. Probably Janeway meant that they had no way to replace the torpedoes because they had a finite supply of antimatter. But they could've traded for a new supply, or for substitute weaponry.
Personally I wish there had been more depiction of the crew trading for replacement parts. I once wrote a spec script for the show in which they came upon a colony of Cardassians taken by the Caretaker (leading to conflict with the Maquis) and ended up taking a couple of the Cardassian shuttles with them at the end to replenish their supply. It would've been nice if we'd seen the ship's systems gradually getting upgraded and replaced with various bits of alien tech they picked up along the way.
Still, given that they had replicators, I really don't find it unreasonable that they could've replaced any equipment aboard, given the necessary raw materials. I mean, replicator technology has existed for decades as of the series' time frame. It stands to reason that by that point, their technology would be designed around replicable components, so that any necessary parts could be easily replaced.