I thought that with our hamster when we hadn't had him long too. Their seemed to be less hair where his ears joined his head and I thought he had little warty lumps there too, but it turned out to just be part of his ears (the lumpy bits)
The hair did go a bit thinner there but has stayed the same every since
So is it actually a bald spot or just a bit thinner there? If it's just one ear, and not both, it might be as Cypher says - he has rubbed up against something, but it would be a good idea to have a vet check and have mites ruled out eg.