Trigger Warning: Nerdy Pedantry.
ST "replicators" would be more properly called "fabricators". Replicators make more of themselves- they replicate. (see StarGate replicators for an example. or any of the NanoGoo scenarios.)
Fabricators on the other hand might be able to make more of themselves, but they're cheifly designed to make other shit- that is to fabricate.
In universe, I'm just going explain it away as, "This is what happens when you let politicians name shit."
As a side note, regardless of what ever you want to call it; why the fuck would you as a ship's designer have access to this technology and not literally integrate it into every aspect of you ship? Especially if you can go the other way- recycle matter back into energy.
grey- and black-water handling would literally be eliminated at the source. other trash, too. Armor plating damaged because Ryker boned the wrong chick again? replication units in the hull replace it automatically. Worf blows his load and you're now out of torpedos? Yeah. who cares, just salvage their hulk and make more.
Wesely crashes yet another shuttle because he's a kid? oh well. it's a good thing Earth has a lot of rivers.