I use the clear gorilla glue to fill in porthole windows, but you need to lay her on her side. put some plain old tape (masking, cellophane, what-ever) on the inside of the hull over the windows. Using a bar straw or toothpick, fill the holes with the clear gorilla glue. When it hardens (overnight), peel off the tape. It does a good job of looking like glass and diffuses the light.
For the lower decks, don't forget to black out a few of the portals here and there for an authentic look. People did sleep (contrary to the movie, where they partied all night).
Bob