I think that the idea of there being difficult-to-impossible elements to replicate is consistent with canon at various points. Even so, unreplicable elements, if there are any, wherever they are on Star Trek
's periodic table, might still be mined, traded for, etc.
So, I agree that it's perfectly reasonable that torpedoes can be replaced eventually.
Same goes for shuttles, too.
But, what's weird is that the show-runners thought it was a good idea to say what they said in "The Cloud" in the first place, especially the way they said it. It seems like just a cheap way to underscore how bad it was to be stranded in the Delta Quadrant, as if it wasn't clear already.