I don't see a point for having jumpers on the ship. The nature of the Destiny's mission makes them irrelevant, as it seeds habitable planets with stargates, then hops back into FTL and moves on. I don't know what you'd need jumpers for. You can just gate to a planet for a while and then go back to the ship.
I thought it was said in the episode that the plan was for the Ancients to board Destiny again at some point?