The Coral Reef restaurant and Aquarium tours/diving tours are totally unaffected. I verified this with Disney since I have ADR's there for September. The Coral Reef is in a seperate section from the attractions and the attractions cannot be seen from the Coral Reef. The Aquarium will still house the fish and is not being changed or renovated.
The renovations are on the Living Seas attraction and displays area including the Crush Turtle exhibit.