a- is a prefix often used to mean "without", I think would be the most correct definition, without looking it up. Atheism, asexuality, amoral, atonal, etc.
So what the hell is with the word "acorn"? "Without corn"? Is that what's behind that object's name? "Hey, what is that thing?" "I don't know, but one thing I know is it has no corn. We should call it an acorn."
Yes I know I could look up the origin of the term, but where is the fun in that?