:agree:
what he said.. absolutely use hot glue if you're going to be working with cardboard. Use the tip of the glue gun or a hot wire tool to smooth down the seams where the hot glue beads up... or you could always just use a heat gun and a spatula.. anything to heat up/flatten out the glue the beads up around the seams.
this can also be done to fill in any gaps you may have between cardboard pieces, since pepakura patterns don't allow for any thickness to the material you're working with, you kind of have to alter on the fly by a little bit a lot of times.