It is very possible that he has developed a sensitivity or intolerance to an everyday item that he has been around his whole life. It may have been causing a very small immune system reaction that his body was fighting reasonably successfully and so it had gone unnoticed. Unfortunately, once the body decides that the substance in question is now a source of danger because of the antibody levels that have built up - you now have hives. Your vet may do a test (or series of them) to find out what he is allergic too. Another thing that he might do is to draw blood to see if your horse's blood counts are normal, if the hepatic levels are normal, etc.
As far as comfort for your horse - get him out of the sun, get him clean of repellents etc, Make sure that his skin and coat do not get too dried out. A body wash made up of a few ounces of a cooling linemint (and a little vitamin e if you have any) sponged on daily or as needed may help with the itching somewhat.