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
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
Now, which computers need this?
Tuesday is Soylent Green day.