I have no idea about the other stealth problems, but I know how to prevent using a computer (or other things) if npcs are close to it.
If an npc operates a compute or anything else, there is usually an interesting place for that. So all we have to do is find these places and add
"OnNPCArrived" "Computer,Disable,,0,-1,,"
"OnNPCLeft" "Computer,Enable,,0,-1,,"
Oh, and to avoid problems the other way around. I.e. the npc going to the computer while the pc is hacking, the computer should have
"OnUseBegin" "InterestingPlace,Disable,,0,-1,,"
"OnUseEnd" "InterestingPlace,Enable,,0,-1,,"
Now, which computers need this?
-Arthur?
-Dane
-museum security