End of the day, you are going to get hit occasionally, or at least you might. It usually won't be too hard or direct. It's about the same chance as any other sport you play - people throw around limbs and objects, eventually nuts get hit. But you get a little more used to it (as much as possible at least, it's never fun), and as said above, way better at defending it yourself. Plus your opponents will be better at not hitting you as they get better.
Basically when you are going to see people getting hit hard is white belt v white belt. Just don't fight really stiff (no pun intended) or at 100% strength, and focus on technique over power, and you will avoid the most common way of getting hit there: doing it to yourself. You are going to be more annoyed with the irritation of the cup from the movement of your thighs, and when your cup gets into one of a few weird positions (sorry to get graphic) like it's edge over your nuts or turned sideways, it'll hurt way worse than a quick shot.
...Gotta say, if someone were to design a BJJ cup that was actually well done, I bet it would sell...