I appreciate the suggestions but I’m not a clicker training person 
I had a welsh driving pony who wouldn’t go near water either. Shaking, rearing and spinning is even scarier when in a carriage!
1 winter turned out in a pasture cured him. He had to walk through a deep muddy area to get into his warm, cozy little stall with grain. Now he doesn’t look twice!
Definitely let him work it out on his own. Turn him out when it is raining if the weather is warm enough, put him in a paddock with some puddles, and he’ll sort it out. If he is as shaken as it seems, pulling him over tarps or trying to pony him will just frighten him more.
Every horse has a glitch… if yours only has an aversion to water, I’d say you came out on the winning end!
Did you try bathing him with very warm water? I’ve noticed that makes a big difference to the behaviour. Ditto fill a spray bottle with very warm/hot water.
What worked for me with a horse that didn’t “do” water, ditches, or puddles, was to turn him out and rig the fencing such that he had to cross a big boggy ditch if he ever wanted to be fed…worked like a charm - it took him all of 10 minutes to figure that one out, and he’s never looked back. It was much easier for me to let him figure out how to get over his angst than to persuade him to think my way.
Hard to tell, but from your description your horse is being more uncooperative and/or stubborn than scared, and the fact that giving him a timely smack convinced him of the error of his ways makes me think you’ll overcome these issues eventually.
Good luck! Can’t wait to hear how he survives his first shower of rain! 
RAIN?!? We don’t go outside when it rains.
I actually realized I had been SUPER sheltering my horse. I guess I was becoming a sissy in my old age. So, this year we did work outside in the rain. And this winter we may actually do some snow. Not alot of snow. but some snow.
