What kind of boat are we talking about? If you're talking about polyethylene, I would want it on edge. No matter what it's made of, I wouldn't put it under black plastic unless it is completely in the shade. A black tent would become an oven if sun gets to it.
In any case, I don't see any advantage in hanging a kayak as opposed to simply constucting, or buying a proper rack with nice soft supports. I built a storage cart that holds three large kayaks. Two of them rest on their edge on nice soft foam rubber and the third one, which is fiberglass, sits upright on two minicell foam perches.
My yaks are kept inside, so I don't have to cover them, but I think it is very important to keep the sun off them as much as possible. Even fiberglass will fare much better without constant sun and in my opinion, sunshine is deadly over the long run on poly boats.