I'm not sure about this, but I believe Lady Vengeance (the level) is being used multiple times as a level templates, whereas the doors, hatches etc more likely are bound to the main level they're in. That way, they can change the hatch from Fort Joy to a new version of the lower decks in a later stage in the game. The story is built when loading into Fort Joy the first time, but also exited the moment you leave it. If all this is correct assumptions, the hatch would be removed if you have any mod that makes you leave the Fort Joy level and come back later, that'd likely remove the hatch.
Why it'd disappear in vanilla game though, I don't know. Could probably make a quick mod to fix it, but if it's gone there's probably something broken about the story build to begin with.