you don't have to explode them (I know I did a few that way) But some/most N64 boxes the cardboard insides pull out and you can just lay them flat with either the front and a spine or the rear and a spine then scan the other side. Some of the boxes the inside cardboard does not come out, so you can't do it that way. (So you end up scanning the front,rear,spine)
Please don't destroy your boxes.