I love to go in Sept. (check out my siggie) and yes it is hot and humid but I still enjoy it. And I'm from So Cal. where we have very little humidity (In fact, we are scheduled to have some later this week and it's all over the weather report!) Anyway, as others have said, T-storms will roll in most every afternoon but usually only stay for awhile. There are exceptions such as last year when we were at the first
MNSSHP and it poured-for hours, and the lightening was the most I've seen in all my trips there.
We usually go to both waterparks in Sept. and that's one excellent way to stay cool! We love

TL and BB!
AK is the hottest park-with all the vegetation it has it's own micro-climate.
I do the parks at WDW completely different than I do the local ones here. When I'm at WDW I do wear some makeup but I don't normally wear that much to begin with. Make sure you wear water proof mascara if you want to have any on by the end of the day. The rest of your makeup will be gone. I also will wear a baseball type hat at WDW. Once my hair gets wet, I'll usually put that hat on, or wear it up with a big clip. I don't care as much about how I'll look, it's just too hot. But you can always wear your sunglasses in your pix and look great! I also waer tank tops most of the time, which I rarely do at home.
Ditto about drinking plenty of water. We actually drink very little soda during the days and do water. All the food places will give you glasses of water for free! And if you want flavor, just add those ind. flavor tubes-my DD8 loves them. I also carry a ziploc with a washcloth, or one of those quick drying towels (like you use to dry your car) in it. Feels great on the face, neck, and arms when it gets really hot. And you can even add ice to it to make it more refreshing.
The mister fans are great. The ones WDW sells are pretty big-you can buy smaller ones. Also you can carry around (clip it on) one of those small, individual fans. Some people bring those neck coolers, but I've found that a nice cold towel works just as well, or better.
Wear waterproof shoes. I now only wear
crocs. My current ones are the Cleos which are more stylish than the Beach ones and even look pretty. I can walk through any amount of water wearing these things and never have to worry about having wet socks! They are also great wearing in the waterparks-no water shoes necessary. If you are going to wear sneakers with socks, bring along an extra pair of socks with you to the parks and pack at least 2 pairs of shoes so you can wear one while one is drying. If they get wet, stuff them with paper towels so they'll dry faster.
Take a break during the heat of the day. Go back to the hotel to swim. If you stay in the parks, find a nice, a/c inside location to have your lunch and later a mid-day rest/snack. If you go back to swim now that they will close the pools if lightening is detected nearby but once the threat has passed, they will re-open.
We like to go to one park in the a.m. and then take a break after lunch. Then we'll usually head out to Epcot (unless there's a EMH PM somewhere) to end our day after it starts to cool down.
AK-Pizzafari at AK is a great place to take a mid-day break. Since AK is only open until 5 (except EMH) you probably won't leave there during the day and be able to make it back so plan on staying all day. Another great place to cool-off is the Finding Nemo show. And it's a great show as well. As is The Lion King. Both, IMHO, are not be missed and are a great place to cool off during the day.
EPCOT-Check out Club Cool for some wonderful A/C and free samples of Cokes from around the world. The Energy Adventure with Ellen is a good ride/show to do during the heat of the day. It's all inside and takes about 45 min. Innoventions, West and East, have some interesting things to do/look at and it's nice and cool inside.
We take advantage of the PM EMH. But then again, being from So Cal., with the 3 hr. time difference, it's a no brainer for us-while the AM EMH is tougher. I love the parks at night.
There are locations at the parks where you can get your body wet-do it-it's a quick way to cool down.
Wear, and reapply, sunscreen. Wear a hat. Drink water. Take breaks. Water play. Have fun. Keep to the shade. Ponchos.