I personally probably wouldn't want to... however, besides the stress of handling them during the time you are painting them I'm not sure if it would hurt them or not...
Does the shell "breathe" any- allow for gas exchanges- or is that all done through the soft tissues and bodily openings? Most animals skins "breath" somewhat- but I don't know if shells do.
People use nail polish as an aide in fixing damaged shells- but I'm not sure if coating a shell would have any negative health effects- assuming whatever is used isn't toxic before or after it dries. I think it might depend on if any gas exchange occurs through the shell.
A few dots of paint is unlikely to hurt though if you're just after cataloging the snails for identification purposes and tracking purposes.
If you're planning on painting an entire shell- you'd constantly be having to do touch-ups as the snail grew.
Unless someone in the know though knows that it is safe- I wouldn't paint your snail just in case... if nothing else- you'd need him/her out of his aquarium needless handle and needlessly stress him whilst painting and waiting for paint to dry, etc.