The admiral's missing a large chunk of his body...
He's not. It's just colored black and it's blending in with the background. If you're having a hard time seeing it, try turning the brightness on your monitor or clean your glasses. It's there. A lighter shade of black could have probably been used I admit, but hes definitely not missing a part of his body.
wow did the admiral made maya mad so he could come and repair akagi?
Even better, Maso TTK disappeared from the anime for the last few episodes not because he was abducted by the Abyssals but because he was personally scouring the deep to retrieve Kisaragi.