Ick, I would definitely let your vet know about it. Yes sounds like he is certainly deficient in a vitamin and more! Is he getting enough forage to eat? Ribs showing, rough textured coat? Is he getting unlimited water, how about a salt block? This sounds alot like just malnutrition to me.
If you want to help regrow the hair and condition the skin topically as well, try extra virgin olive oil (organic or cold pressed is in a more original basic form and is best to use) massage it into his skin on all of the bald patches every few days. Hair should start growing back in no time.
Viodine is a medicated shampoo for rain-rot and other skin problems if you want to look that up at your local co-op or Tractor supply.
JeffersEquine.com also has it.
Definitely talk to your vet about it though, that really sounds rough!
