What I want to know is do they purposely over book a room category?
I used to work at the Disney Reservations Center. I trained Sales Agents and answered calls occasionally on days when classes were canceled due to extremely high call volume.
There are only a few people that can answer your question. Namely, upper-level management at the Resorts and analysts/managers in the Revenue Management division. None of those people would ever share that information because it's considered proprietary information.
Sales Agents do not have access to that information. I didn't have access to that information, either (and I had significantly "higher clearance" because of my job in the Training Department).
That said, the majority of guests going to Disney World want multiple beds. My educated guess based on prior jobs working as a hotel Revenue Manager is that it's unlikely that Disney significantly overbooks king-bedded rooms.
Things happen. Plumbing/electrical/etc. issues can occur that will put a room (or possibly even an entire wing/floor/etc.) out of commission.
Maintenance issues do pop up occasionally. But from working in hotels for over a decade, I'd say that guests overstaying their reservation is the source of 80-90% if these types of issues.
Even with proof that the guest is overstaying, hotels are reluctant to evict an in-house guest. It's a messy process with the potential for bad PR. Additionally, some locations require the police to become involved in order to remove a guest because it is considered trespassing. (I have no knowledge if the counties where Disney World is located requires law enforcement to get involved. I never worked in Resort operations when I worked for Disney.)
My best guess is that when a booked category isn't available at Disney World, it's more likely to be because of a guest overstaying a reservation than a maintenance issue.