Because Gabbits can?
I think it might have been to differ Abe and Munch a little more gameplay-wise. If Abe could swim, then Munch would lose one of his unique abilities. But... this isn't all true, Munch would still be able to jump out of the water into the air and stuff. Other thing I can think of is that Mudokons evolved from birds and some birds can't swim too well.