Along the same lines I doubt they can just "replicate' shuttles again coming back to a quantum-level complexity that would be lost in the replication process or a cost-benefit situation. It's not worth replicating an entire shuttle when you can just go to a starbase and pick one up at no energy cost. (Energy better spent for other things like food, propulsion, etc.)
Voyager managed it just fine. They built their super shuttle in the space of a single episode, and unless they had like 50 plus shuttles crammed in every nook and cranny of the ship, they were rebuilding those things non-stop.