The Company Store is more than just a souvenir shop -- it's a mini Apple Store. You can most certainly purchase more than shirts (some hardware, iPods, software, accessories, etc. The exception is that it does not have a Genius Bar.
Wouldn't surprise me if the forthcoming new Company Store (located at their new campus) wasn't a full-fledged Apple retail store. It'll probably be located separately from the main spaceship building just like the new keynote auditorium (no more Moscone West or Yerba Buena).