There's a simple reason for why Donald wears a towel when he gets out of a shower and why he wears a swimsuit when he goes to the beach: rule of funny. Also, there are two reasons for why Donald doesn't wear pants; 1) it looks silly (just look at Howard the Duck), 2) according to the animators ducks communicate with their tail feathers and thus drawing them pantless provides some comedic scenes (just watch the "Mr. Duck Steps Out" animated short as one notable example if you want proof).
