A long time ago, in a galaxy far far away, I purchased the disc version of Aperture 3. After updating to Mavericks, and updating Aperture to ver. 3.5, Aperture now appears (along with all the iLife and iWork app's) under my Purchases.
I have to wonder now if the next version of Aperture will be free to current owners.
This was also how I purchased Aperture, way back when. Turns out this is Apple’s way of getting their users who had disc based version into the same system as their Mac App Store users.