This year, i’d be very surprised if any of the mapped streams dry up. There is always the chance of a snowstorm in September, but generally they are short and melt within a day or two that time of year. I’m afraid i don’t have info on the resupply points closing. I’d think at least Tuolumne and Red’s Meadow are sure things to still be open. VVR and MTR you might want to call ahead.
I’ve only been on the JMT in early September. It was a perfect time of year. I bet late September would be great too. The only slight detraction i can think of is the days are getting shorter fast that time of year.
markv