I've been keeping spare weapons and items in piles in the elevators in the System Shock remake.

I've found them to start vanishing recently. I didn't even notice until I'd already saved over the file, but my upgraded shotgun and magnum are both just gone.

a while later and the entire elevator is empty. I'm so pissed off, I'd have to restart the whole game to get my stuff back at this point.

The best place to keep your extra stuff in System Shock Remake is probably the room on Maintenance level with Recycle station and big elevator to Storage and Filght Deck levels.
There are 4 storage boxes in that room, that should be enough for most players.
You also may leave big items like weapons simply lying on the floor there.
Don't leave them INSIDE the elevators though.

https://www.reddit.com/r/systemshock/comments/146wdyi/bug_items_in_elevator_have_gone_missing/