It can be, though the school system has changed, so a number of people are school by then. It will be moderately busy I should imagine, but because of hurricane season, most Americans are not really drawn to WDW in September (hence why they often offer free dining).
IF you have tickets, I would still go to the parks, but maybe plan on an Epcot or Animal Kingdom day where the crowds don't matter as much. Most long weekenders tend to go for the MK or Water Parks.
