For what it's worth, it's happened to my company (a smaller company sued by a larger competitor), and the litigation has dragged on for almost three years now without going to trial.

I've heard of other similar incidents as well. They're far more likely if you're going into an existing market against well-funded (and shameless) incumbents than it is if you're in a nice market.

You're correct that the rational response is to not worry about it, simply because there's nothing you can do about it as a software startup. If someone wants to sue you, they will, no matter how far you go out of your way to avoid violating patents. So you just kind of hope you don't get unlucky and get sued before the company becomes big enough to file their own patents for defensive purposes.

Just because something happens infrequently doesn't mean it's not a real problem.