The manatees are in the same basic tank as the turtles at Turtle Trek. This exhibit wasn't shut down in December that I recall, although periodically some manatees may be moved in or out of the area for medical or testing procedures.
I can't recall any other place where someone might have seen manatees at one time that would be closed now. The penguin area is definitely closed, and certain rides and attractions are down for yearly work for a period of time. That is all I can think of.