Firstly, whatever you do, remember that those boxes have a value. Anyone selling ships through the post faces the problem of how to safely package them, and there really is no better alternative to the original box. Anyone storing ships (pending that display that they haven't built yet), will want to store them safely. So, if you do dispose of them, sell them!

Secondly, if you keep the boxes don't break them down whatever you do, because who will have the time to reassemble them? The other thing is to check whether it is easy to match the models to their boxes. Ask yourself whether someone else with no specialist knowledge could easily re-unite the ships with their individual boxes? If not, a seller is likely to just shove the ships into the first available box.