According to 9to5 Mac the self-checkout system is being dubbed "EasyTheft."
I think it will be tweaked. Apple Stores are often mobbed, not only during the holidays (when most stores are), but also during product releases. While it would have been nice to have this system when I was shopping for a new case for my iPhone 4S (5th Avenue had the one I wanted, but there was no one around to check me out, UWS had people who could process payments, but not the case I wanted), shrinkage could be a real issue here. It will be nice if it works, though.
The in-store pickup for online orders is long overdue, and very welcome. It was a short "pilot," having just started in San Francisco last week and New York yesterday. However, I'm guessing Apple figures it will save enough in shipping costs to make it worthwhile (perhaps the "free" shipping on orders over $50 will eventually go away).