As SQUIGGLE noted, the season is officially from June 1 to November 30 with its peak around September 10. Your highest chances for an altered itinerary are between mid-August and early October. No cruise has ever been cancelled, but they do occasionally go in entirely different directions to avoid being anywhere near the storm. In addition to the "mystery cruise" that went to Castway Cay twice and San Juan once, one of the Wonder cruises this past Fall went to Charleston, SC.
Also note that you can have rough seas all during the season. The last storm of this past season lingered into the first week of December. And even though the actual storm was nowhere near the ship, it still caused rough seas all over the Caribbean.