Apple is planning to offer a personal set up service
Apple has been slowly decreasing the amount of retail floor space used for software over the last several years. Software boxes used to be much larger, but have slowly gotten smaller in recent years, and some of Apple's own software, such as Snow Leopard and iLife '11, come in boxes just large enough for the install disc and a small booklet. Heck, the system restore disk for Apple's latest MacBook Air models—which lack an optical drive—comes on a small USB key.
Beyond the hurdle of making all current retail software available via the Mac App Store, the realities of current broadband speeds in the US places limits on distributing software that relies on gigabytes of graphics, audio, or video files. This includes many creative media suites, but also includes things like Apple's Jam Packs—multi-gigabyte collections of audio loops for its GarageBand and Logic audio editing software.
The time for all-digital software distribution is coming
Omni Group CEO Ken Case told Ars at Macworld last month that it has replaced all retail boxed software sales in the US with Mac App Store distribution. While not all Mac OS X developers are ready to rely on the Mac App Store as the sole distribution source for their software, most (like Omni) do already rely on online distribution via their own web-based or in-app purchase options.
Apple would need to come up with a solution to distribute software like Jam Packs and OS upgrades and get other vendors like Adobe and Microsoft on the Mac App Store train before before dropping the software section from its stores entirely.