The 8th ave to 7th ave tunnel exists but is now behind plywood.
Other closed exits: Howard AVe (Ralph ave A line), Broome St (Delancey J Line), Classon Ave (Franklin A Line- even tile is gone), 94th st (96 C Line). A check of the station-by-station pages will list those we know about.
Oh yes-- Metropolitan Grand G line is the latest addition. Only the Metropolitan exit remains. The Grand exit is now closed although work satirs remain fromt he platform,and the middle mezzanine is the Brooklyn Transit Bureau Task Force location and storage and employee facillities.