Normally the only major gaps that would need filling will be on the underside of the deck on the back deck if the design makes a sharp corner that's often tough to get tight on the inside. Most hull joints will easily fill with the epoxy of glassing.

To avoid any extra work what I do is: I have my glass dry and laid out on the underside of the deck. If I need to fill a few joints that are on the shear bend and I know gravity won't be working with me, I mix some epoxy fill (sawdust - whatever) and pull back the glass cloth and fill them then. Pull the glass cloth back in place and glass the underside deck right over the filler.