The bottom line is this: no limitations have never been explicated for the replicator.
As I mentioned and you glossed over, so I looked up specifically:
JANEWAY: Those gel packs run half the critical systems on this ship. Once they run out, thatís it. We canít replicate new ones
VOY, Learning Curve.
Now, if it were possible
to replicate new gel packs, don't you think they might have bothered to include this possibility in the replicators on board a ship which relies
on them? To me, the meaning of this line is clear: they can't be replicated. And mentions elsewhere on Voyager of searching for dilithium strongly suggests this can't be replicated. Mining might be cheaper or easier back in the AQ but if it could
be replicated, wouldn't Voyager have tried that?