There is a lot of debate about the origins of the word, and the skull story is a nice (but brutal) party story. Let me give you another version.

Back in the days people were drinking off bowls, instead of cups as we do today. And guess what the danish word for bowl is? "Skål".

A "skål" is a flat version of "trebolle". You can see one if you Google Image search for "trebolle" to get an idea of how it looks.