Well, given that there is such a long window of time in which they lay, and the variable of weather, I would guess that a good many eggs get rained on.
Plus, given the fact that many other pythons, granted from more humid areas but genetically close to ball pythons, have their eggs rained on regularly with no ill effects, personal experience with balls and extrapolation from other species, a bit of water isn't going to hurt the eggs any.