Which would give you a nice malus on your morale for killing someone innocent. So that’s a no-go, unless you’re able to provoke them into attacking you first. And even then, you do not want to start a fight with someone who might have stolen one of your mininukes or badass gun.
I usually play with a mobile Base, meaning a big vehicle with tons of storage place, so I don’t really have a problem with NPC’s stealing stuff, as they do not rummage through vehicles (they do go right through vehicles though, if they find doors, and leave them open, which can be annoying as hell.)
As others already said, you can always use Crates and/or special furniture where you can’t see the items from far away. Put them into a room with strong walls and 1 door for extra security.
Another interesting Idea would be the following: Make a base without doors, and make an underground tunnel leading to it. Not only is the underground tunnel safe because npcs and monsters don’t switch Z-levels unless they follow someone, I’d also assume it would stop npcs from breaking in, when they have a clear way around it. Path of least resistance and all.
Of course, traps would be the most useful way of…getting rid of thieves. You won’t get the ‘killed innocent’ modifier from traps, and you will get their equipment - and their bodies, if you like feasting on humans.