If he yelps. he's in pain. I would have the vet check him out. If water was in he's ears, he would try to shake it out. I don't think I would take the risk of it being something else. Give your vet a call and see what they say.
As far as hair growing back, it takes two -three months, depending on how short they trimmed it.
Good Luck, please keep us posted on his ears.
