I did not notice Mickey Waffles missing, but I did notice the breakfast Buffet get cut in about half at Fort Wilderness abd they got rid of the french toast.
Even if they aren't on the menu, ask your server and see if the kitchen can help out. We've had restaurants serve us the waffles without complaint a number of times.
Last time was at the Epcot princess breakfast. That one is served family style, but curiously there are no waffles or pancakes on the normal platter. All it took was asking our server and we had a plate of 4 waffles a few minutes later.
Felt bad for the kitchen staff, though. I think some of the other nearby tables noticed it and before long they were bringing out more plates to others. But seriously, I think they are used to it. Doesn't take much effort to mix up a bag of batter and cook some waffles.