Here's someone who appears to have given some deep thought about the origins of the wink, surveyed friends about it and then blogged what he learned about it:
http://www.howardism.org/thoughts/001450.html
And here's someone's response on yahoo to a similar question about four years ago:
Winking, how delightful of a gesture! I guess it is an innocent little gesture of seeking intimacy with someone else.
I have something in my eye. (I am physically vulnerable right now.)
I want to blink but I need to see what is going on at all times. (I don't trust you with both eyes closed.)
I just told a joke and now you are in on it...a sly wink in the presence of other people. (I trust you with secret information.)
I'm just kidding about what I just said. (I want you to know that I am not revealing my true feelings.)
I am flirting with you. (I want to get closer to you.)
I guess subconsciously when one eye is closed, it is a simultaneous awareness of something outside and inside. And also when one eye is closed, it means a bit of trust is needed from the other person that they will see what you don't while they aren't looking around.