if Watch is just the beginning of Apple getting into wearables and if Apple gets into first party HomeKit hardware (there were rumors to that effect) I can see Apple stores selling fewer and fewer third party devices (outside of iPad and iPhone cases).
You are right. Apple Retail Store shelf space is limited in most of the stores. In the future, they need to be smarter about allowing "retail access" to 3rd-party accessories. They will eventually run out of space in trying to showcase all those products.
One idea I have, is that they could install a few "shopping kiosks". Like they can have a limited selection of say OtterBox (and other brands) iPhone cases on display. And next to the physical products, there is a small kiosk. You simply browse the exact type of Otterbox case you want, the exact color, and then order it right there. The Apple Pay terminals would give this a dose of secure transaction, since no one in the Retail Store will ever see your credit card info or your debit card passwords, etc.