OP, I've heard those naked spots be attributed to the horse shedding out faster than the summer coat is growing in. It happened to my mare one spring where her entire belly was fully hairless but the rest of her had hair. She's a very white gray so she looked absolutely ridiculous.
Of course, that did happen the spring after she was allowed to get about 200-300lbs underweight (I was boarding her, it wasn't good, etc) so maybe it was a nutritional deficiency.
In any case, the hair was grown in in about a few weeks, she just looked ridiculous for those weeks in between.
I wouldn't worry too much about it if he looks healthy and the hair looks healthy. :)
Fabio - 13 year old Arabian/Lipizzan gelding
Rest peacefully, Lacey.