Here's some updates. For the prop covers I think this is the best I can get without blocking off the entire duct. The covers pretty much sit on the outer rim of the duct and slide in along the supports. It's going to be a chore to animate but it should look good in the end.
And just like the Kraken the conning tower is going to have an observation section. Also if you look closely at the top of the tower you will see a small mount for one of the browning machine guns. I'm going to attempt to work in something else rditto suggested about guns that can be taken below deck when diving.
