About the dupicate stores, I kind of figured it was an issue like that. It sort of happened to me as well but mine was due to an internet lag.
Have you played Willow's Collectables yet? I'm curious to see if the employees and guests act the same in your game as they do on mine. Because on my game, the shoppers do disburse. Yes, there is usually a clump of them chatting it up with my employee or me (which I find convenient since we're both presumably talking up the store) but they do scatter pretty well in my game.
As for your mall idea, that would be insane for a single household to manage! So yeah sounds like a serious challenge. Great idea for a community lot though.
As for the employees, I started another thread a while back about visiting Willow's Collectables with a different household and there were two employees although I know that the Wentons only hired one. So I think the store size determines how many employees perhaps...