Bad News: September is the peak of hurricane season.
Worse News: With La Nina forming in the Pacific, hurricane season is expected to be worse then normal.
However news: Last year the "experts" all predicted a terrble hurricane season and they were 100% hugely wrong, it was actually very quiet.
Bad However news: The quiet season was due to an unexpected El Nino. La Nina is the opposite of El Nino.
The reality: Even if a storm or two blows up in Sept, the cruise line will alter the itinerary, you will not be put in any danger. No storm will hit every Caribbean island, so I would go anyway since cruise prices in the fall are as low as the get.