Pools are usable for both. Sep typically has high temperatures and high humidity daily. You expect days to be hot but some are shocked by how hot and humid the evenings remain (as put once, in Sep you can sweat standing still outside at midnight). Oct remains hot, although a decrease somewhat as the month progresses, but beginning in early Oct, that nightly humidity usually decreases and evenings become more pleasant. The hurricane risk is higher in Sep, although still some risk in Oct. Sep often gets a lot more rain than Oct, with a higher risk of having a night time activity, such as Fantastic, cancelled as a result. Bottom line, for better weather choose Oct but Sep is usually still doable.
As to park crowds. October tends to be fairly large although not stifling, with some lengthy stand-by lines (an hour or more for premier rides). Very end of Sep approaches the Oct size. But second and third week of Sep are among the best crowd times of the year -- e.g., my last Sep trip was third week of Sep 2018 with premier rides (other than Avatar Flight of Passage) having stand-by lines mostly in the 30 minute or less range (Flight of Passage exceeded an hour) and most others 15 minutes or less. Sep can be somewhat worse for getting dining reservations if Disney has the free dining packages for hotel guests. And when there is free dining, I have noticed that what is offered, such as for the buffets, is not as good as other times.
