Yes, the streams closed to fishing are closed to all fishing. After 9/30 you limited to the special regs areas. Plenty of good water though. Another warning is that the NYS fishing license goes from 10/1 to 9/30 so if you fish into October you will need a new license. The Delaware branches have parts that are open past 9/30, but the regulations are fairly complex so check carefully.
Fall can be great, can be tough. Water can be low and clear and the fish have been fished over all season, so it isn't generally an easy time to fish.
Love if they hit isos, since they are a bigger bug. Cloudy days will be BWOs, and there are a smattering of peach Cahills, caddis, terrestrials, etc.
One thing I like is that the rainbows move out of the Delaware system up the East branch and into the Beaverkill. Fish the fastest water you can find with a nymph and you may find some decent wild rainbow fishing,