Ships never go "through" a serious storm, like a Hurricane. The are in satellite contact with the Weather Service, and simply move out of the route of a hurricane.
The worst that can happen is that they may have to substitute a new port.
I was in the Western Caribbean when a major hurricane hit St. Thomas -- where we cruised, there wasn't a cloud in the sky.
You may want to book the Western Caribbean, since hurricanes typically strike in the eastern Caribbean. I personally wouldn't hesitate to cruise during this time.