FRS Ferry Chances of Cancelled

I don't have any good advice about likelihood of cancellations, but two possible backup plans come to mind.

One: I've heard people suggest going to Algeciras to cross to Tanger Port because those ferries tend to be bigger than the hydrofoils on the Tarifa - Tanger Ville route and are more likely to still be crossing.

Two: You could stay a day or more in Tarifa and try your luck the next day. Upon arriving, I remember wishing I had time to stick around a little longer. Lots of cute clothing boutiques, fun restaurants, and beaches with kite surfers. I got the sense that it wasn't a museums-and-churches destination so much as a pleasant beach vacation destination.

Late September still has generally good weather in that part of the month, I wouldn't worry too much. The other poster has outlined contingency plans.

How about late October?
We're planning on spending part of a day in Gibraltar and catching a late afternoon for to Tangier for 2 nights.

The Straits of Gibraltar is very windy throughout the year and the winds are frequently strong enough to cancel crossings, sometimes for several days at a time. I've stayed along the coast of the Costa Del Sol at various times of the year and there is no specific time of year when the winds are worse. All I can say is that they tend to become stronger during the afternoon.

Do you have the whole three nights in Tangier? If so that's a lot for a place that I wouldn't even consider worth a visit. My backup plan would be to not even consider Tangier and stick to Spain as it has so much more to offer however I know that the temptation to "visit Africa" is too big a draw for some people.