There are some people who swear that vacuum aging is best for long-term aging. I'm not one of them. As someone who brews his own wine and beer it seems counter intuitive to think that airless aging will improve flavor because fermentation depends on air. That is one of the reasons wine bottles have a cork - the cork actually allows air exchange. But this is just another theory.
IMPO I prefer aging in the cedar box for the purpose of imparting the cedar aroma as well as the protection the box provides. Also, the box may be useful for buffering climatic changes to a limited degree. But when it gets down to less than half a box then in the tray is fine. If you want to age them longer, say 5-10 years, then it propbably makes more sense to leave them in the box with the shrink wrap on.
As an experiment I put a bunch of cigars in a ziplock bag several months ago. I didn't vacuum it, but I squeezed out as much of the air as possible. I'll probably wait a year and see if this has any affect. My guess is the lack of air will actually preserve the current flavor profile and would actually prevent further maturing. But we shall see.