We really need some hostile alians to invest the creepy places on big ships.
These type of things are so much fun!
It's very interesting how people can be counter-instinctively placed into a pleasant, curious mood when they're exposed to environments of a sinister atmosphere... Mysterious, fishy, eerie, uninviting, bleak, dark places where it is always a likely true suspicion that we are at some sort of risk, because "something must be watching".
I myself often go for that in my projects, and always look for that in other games, movies, and sometimes even in real life (I recommend old abandoned factories, those tend to be interesting subjects for art photography too).
Some design choices that are conducive to this sci-fi creepy effect are very dim lighting, lots of large surrounding objects behind which something could hide, and a complex labyrinthine path leading towards the creepy area (so that one can think "If something happens and I need to run, it's a long way back to safety, and there's a chance I might get lost on the way"). You nailed all of these in this ship.
To end with a paraphrase from Ellen Ripley:
I can tell where it is... it's down there, deep in the basement, hiding in the dark, waiting for the right moment.