Kyle, no offence but I think you are expecting alittle too much of this game
You are testing things which are really too complex for this game in which you were meant to get jobs and complete them.
The conquering thing isnt even really worth doing, its just a money drain.
The campaign is the real aim to the game, not conquering cities, unless its a specific quest.
NPC's never pick up weapons on the floor, or at least I have never seen it happen yet, unless its their weapon that was shot out of their hand.
I dont think there is a way to be sure that you steathily enter a city, its just chance as to where the enemies are located.