I stopped playing 7 years ago after getting stuck on the sewer mission. Came back and that worked fine at least. Played another 4h without game breaking issues, but I can't switch bolt weapons separately from torpedoes (all I can see are the 3 torpedo types when switching). Also there's a chef that's in the middle of any place that I dock with. That one's more of an amusing bug than anything.

Edit: scratch that, the Miras quest is bugged.

Further edit: had to go back to a previous save before I went to the search area. When you get there, make sure to talk to your crew, specifically sonar / torpedo. Otherwise you miss the quest checkpoint and it bugs out.