How many other ducks do you have? Could it be that he is being picked on, or that another more dominant drake is mounting him and ripping the feathers off of his head? In one of my Call pens, there is one hen (out of six) that is the drakes "favorite"
and her head is half-bald right now. There is never any blood or anything - he just pulls the feathers clean off her head and leaves bald spots. It grows back when she molts.
I used to have drakes do the same thing to eachother - just a thought.
Besides the bald spots, does he seem healthy and active? Clear eyes, normal poop? Do they have access to swimming water and do they preen and keep themselves in good condition? If not, mites/lice could be a concern. There is a good article on mites/lice that can affect ducks here:
http://www.callducks.net/ectop.htm