It seems likely that the transition will take quite a while… That said, it's entirely like that shelf space freed up from software would simply be used to display more hardware and accessories, or possibly to provide additional working space for training sessions and/or troubleshooting issues with customers.
Deano’s answer to: “Once the new Apple App Store launches, what will become of the shelf space used for boxed software at the Apple Store and other retail stores?”
deano.com 