DS9's runabouts appeared to be named by Sisko, as they had some off-hand conversations about what they were naming their replacements. So for whatever it's worth, he got a say in it after they were already built.
He never did run out of Earth rivers to name them after
In Prodigy, the USS Protostar has a vehicle replicator that it uses to print shuttles on demand. The Intrepid class was fairly resilient and self-contained, so it's a fair assumption it would have something similar, but we never see one on screen or even directly mentioned.
I don't know if I'm just crazy or not but I'm pretty sure you can't replicate shuttles like other things because of their complexity, otherwise they could just make a jumbo replicator and pump out starship after starship
You are right, but also wrong. They cant replicate complicated things, but they can replicate parts of complicated things, and then professionals can assemble them. They reference it a few times. They talk about it when they need a new energy source because they are short on supplies, more than just food is mentioned. That and the delta flyer. They assemble to a degree but parts are replicated and assembled. Otherwise they would care about a lot more things than just energy and fuel in the delta quadrant. I think there are a few things that don't qualify, like the warp coils for the entire starship. But even then they can make shitty coils for shuttles I'm pretty sure.
I may be crazy but I feel like there's a scene in enterprise where they are getting repaired at a Starbase and they show a panel get like replicated/transported to place and then it's bolted or welded in after. They do mention that replicators and transporters are almost the exact same a few times so it's hard to tell.
God damnit it's kinda embarrassing how much I know about Star Trek. I use the show as a coping mechanism lol.
Edit: oh shit gel packs too, they couldn't replicate new gel packs.