Some bus routes run 24/7, mind you not the actual buses. Moving CM's from point to point on property. Then there are at least three different bus depots that I have found. 1) behind TTC gas station. This is the main fueling location for them as well as some parking. 2) behind AK there is the repair facility (near waste water treatment facility). 3) Possibly off Sheberth Rd as well. There may be others too.
There is also totally separate bus transport from WDW property to the Disney College Program Dormitories via TranStar buses which are contracted by Disney, not operated by them. Also on occasion Disney contracts with Mears Transport for overflow capacity transport when needed, theses buses that I have seen are plain white with no wraps. Kinda like Disney Magical Express which is operated by Mears also, but wrapped to look like Disney.