If you type with only your finger pads and your fingers stretched out, even when I get lazy and have long nails, they never touch the keycaps. The only reason why what you mention would happen is if you have nails several inches long or you type with curled fingers. Typing with curled fingers, while more traditional, is apparently quite a lot worse on the fingers, so you wouldn't want to do it anyways.
Spherical caps aren't supposed to be more comfortable, just better looking (not even, in my opinion). They're not sculptured, so they won't feel good on the fingers like cylindrical.