They could do it in the shuttle bay, they wouldn’t need much more space than a finished shuttle takes up. We know they have shipboard replimats for larger things, I figure replicating and building standard shuttle models on long voyages has standardized procedures and steps like Lego instructions. You only need to replicate one piece at a time saving on space. Gotta replace your shuttles somehow on those 5 years missions and the nearest Starbase is months away.