Boxed software is somewhat easy to steal, and takes up lots of space. By moving customers to the App Store, Apple Retail could lower loss and sell more expensive hardware accessories.
I see two big problems with this. Major software suites like Microsoft Office and Adobe Creative Suite will never end up in the Mac App Store. Will Apple still have to sell those titles on physical discs, or will Apple Retail send customers out onto the Internet to order these programs on their own?
The second problem is the OS disc. I think this problem is a smaller one, though. The MacBook Air ships with a locked USB key with the OS on it, and since all Intel Macs can boot from USB devices, I think Lion will probably be sold only on USB key, not optical media.
Remember as well that not all customers are comfortable with the Mac App Store. It doesn’t scale well for enterprise or education customers. While the App Store will continue to improve and grow, I’m not sure that Apple can ditch the box quite yet.