While I'm sure TDC Nala has more official info than I do. I'd say don't count on anything being open. We have been surprised on extended hour days in the past that the Epcot eateries, for example, did not extend hours. At many QS eateries, they make a certain amount of something each day - like say, cake - and when they run out, that's it. So even before the park closses, they may be out of some items.
One place that often bakes 'late' is the Main St. Bakery.
We often do late nights in the parks, and one of the constraints is often our hunger. If you are running around the parks until 2am, you sometimes get hungry at 1am. By the time you get back to your resort, the QS places are all closed. Room service/pizza delivery might be available- but it's pricey and time consuming. You don't want to have to stay awake for another hour waiting for your food to arrive.
Two options that have worked great: a.) Keeping some kind of non-perishable munchies on hand in the room. If you don't eat it during the trip, you can eat it on the way home. b.) Pick up a muffin or something in the park before the eateries close. If it's something like a muffin - then you can eat it late at night OR for breakfast (supplement) the next morning.
One of my favorite evening pick me ups is a hot chocolate chip cookies from either Main St Bakery or Sleepy Hollow.
We've even been known to have a cookie for breakfast. Nothing says WDW like chocolate chip cookies at 8am! (Then again, when you think about it: cookie, muffin, pancake, pastry...are all basically the same thing anyhow. They all have similar amounts of flour, sugar, and egg.