That begs the question, Jo: would a rational atheist indulge in vandalism or opt for a legal protest? There MIGHT be some fringe atheists who might go for it, but if there has been an instance of a religious billboard being defaced (I never COULD stand those "GOD" billboards!), the report hasn't reached my ears yet.
My guess is that when theist billboards are vandalized, it's most often done by other theists. It's not just a question of competing morals you know; it's also a question of competing statistics. There's a lot more theists around than atheists.