I haven't seen anything said about it transferring box licenses to the App Store.
The license for the boxed version of Aperture allows for installation on both a desktop and a laptop owned and used by the same person. One caveat is that it may only allow it to run on one system at a time if they're on the same LAN.
So if you have a desktop/laptop combination and would only be using it on one computer at a time, you're covered.