Hello, I dont know if this was suggested before, but here it goes...
1.
A lock that requires 300% skill to craft (could be a colorised lock icon) and be only pickable with a Electronic Lockpick Mk 2 (and even then 300% skill lockpicker would have lets say 30% chance to open it up)
Why? We all know thieves are a problem of growing factions and some of the newly joined will do everything to steal as most as possible. Having such developed lock would be always a risk for the new incomer to try to lockpick it. More likely he will fail and raise alarm in the faction leaders of a thief inside.
2.
If the 1st is not a good idea, I also suggested some time ago to implement safe (like in Fallout 2 raider cave) locked with dog tags or password (I forgot the exact formula

) and protected by a trap (explosive) would fend off some robbers. The safe would be only pickable by a demolition expert who would place some dynamite on it. If someone without enough trap skill will try to lockpick it or will pull handle (in the dialog, like in F2) the safe will explode