It’s been awhile since we’ve been able to go in September so I can’t accurately comment on the crowd situation. It used to be super low. I imagine it’s still a lot better than October in that respect. Most years if there is a hurricane, the Disney area is not hit as hard as it was last year. Sometimes it will just be really rainy, but the kind of rain that you can still put on a poncho and tour the parks in. In fact, some of our best times have been in the rain when the parks cleared out some. Do be prepared for extreme humidity.
If you’re interested in these kinds of things – the Food and Wine Festival is on at Epcot and Mickey’s Not So Scary Halloween Party is held on certain nights at Magic Kingdom (ticketed event, but a lot of fun to ‘trick or in treat’ in the park). Even if you don’t go to the party, Magic Kingdom is still decorated for Halloween with Mickey Pumpkins, etc. all kid friendly.