The origin of the term is "buck naked" as in "as naked as a buck deer". It originated during a time when people were less urban and a deer or other wildlife were not such alien concepts, and their references were sprinkled throughout speech. "Naked as a jay-bird" is another such cliché. It was further reinforced in its usage by the fact that a buck-skin is similar to tanned human skin. The corrupted term "butt naked" is just another example of mispronunciation that gets ingrained into people's speech,
(I think I just quoted myself, can I give myself rep, or will it just go into some sort of feed back loop?)