Unofficial Fallout 4 Patch

This happens with keys in other locations in the game as well (BADFTL is one of them). I'm not sure whether it's actually a bug or intended. We'd have to check to see if any keys in the game are specifically marked not to respawn to make a definite determination.

the whole loot respawing situation is kinda fucked if you ask me, but a key magically reapearing after you pick it up doesn't make any sense

That is the only way for the game to make sure that there is a key available, While you can't sell them, you can still drop them in a container somewhere and forget about them, and then there would be complaints as well. The only other possibility is to flag them as quest items, but that would lead to complaints too - apart from the technical aspects of flagging items as quest items that don't play a role in any quest at all.

If you go by sense and logics, there wouldn't be much left in your game. After all, enemies should not respawn either - but if you prevent them all from respawning, the game might become boring rather quickly.