We sail quite often during hurricane season (love those off-season rates!), and have never had a problem with rough seas. At least, no more so than any other time of year. On one cruise when we were re-routed due to a storm, we still didn't have any problems with rough seas. In fact, my favorite time to go is late September or early October, the heart of hurricane season. The weather is really hot, which I like, and the days are still long.
I'd agree with mmouse37, book when it works for you, you cannot predict the weather with any type of certainty, and going during hurricane season doesn't necessarily mean you will encounter rough seas.