As Dan W says, flying over a rotating storm isn't a big deal.
If you're talking about flying over a bunch of Cbs, forget it. In the tropics they usually top out way over 50K feet. but the big gotcha is that when building they rise at a phenomenal rate. No outclimbing them and the tops are usually extremely turbulent. Then there are the temperature variations to consider. About 40-50 miles deviation sounds good, at least over the Pacific, I have no idea about the Atlantic.