No, most Americans don’t perceive him as naked, any more than they do Bugs Bunny or other anthro mascots.

I think it’s the accent. His voice actors are pretty hard to understand sometimes.

Interestingly, having only ever introduced to those characters through comics, I never pictured any particular accent and instead imagined them speaking normally.

I'll contribute another anecdotal data point; I've never known anyone even to consider that point of view. It's more that Donald Duck comic books just didn't catch on here the way they did in other countries. But people do recognize Huey, Dewey, and Louie.