Hi there,
I have the same problem with my 4 month old. She wears socks on her hands at night time and when i put her down for a nap. She also had a terrible case of craddle cap (now is almost gone). The reason why my daughter rubs, is to deal with the pain of gas. It's basically a habit that my daughter has developed to deal with the pain. I was exclusively breast feeding and I thought it was the things I was eating. After weeks of not eating this and not eating that, she STILL had horrible gas. I started incorporating formula into her diet, and it helped a little. Now she is on straight formula, and is still having stomach pains. So, I believe that my daughter rubs her face and head out of habit. When they do it as often as your son does, it just sounds like that way. I swaddle my daughter, so the hands stay away from the head. I am up a few times a night re-swaddling her/feeding.
If you know FOR SURE that it is because he is itchy, then try 1/2% hydrocortizone (not on face, just head). See if that does anything.
have you swaddled him before?
Good luck!