The afternoon showers are usually pretty short, 30-45 min but the rain can be pretty hard sometimes with some lightning. And afterward when the sun comes blazing out it’s like a sauna. Make no mistake, late September is still fully summer in central Florida.
If there’s a hurricane it can be anything from moderate rain for a day or 2, to powerful storms with strong winds that force them to close the parks and the airport. Depends on the severity of the hurricane and the path it takes.
Could definitely ruin a vacation, but it he odds of a severe storm hitting during a given week are pretty small statistically. We’ve gone the last 2 weeks of September at least 10 times and been pretty lucky with good weather. We were there at that time for the start of the 50th in 2021 for 9 days and never saw a drop of rain. It’s a crapshoot though.