I did an Archive and Install upgrade of my Aperture drive, mostly to save the time it would take to restore the 150GB Aperture library. I have multiple drives in my Mac Pro, primarily one for Aperture, one for development and a couple of smaller spares for dinking around. It's incredibly useful to have spare hard drives in the machine for these kinds of data-shuffling situations.
The only issue I've seen so far is a problem with hiding applications when working in Spaces. I'm not sure I'll ever get used to Spaces - I have too many years of Cmd-Opt-H hiding and Cmd-Tab app switching ingrained into my memory. The other - trivial - problem was that Aperture lost its serial number during the Archive and Install, because Aperture keeps its serial number file in /Library/Application Support, which gets archived.
Also, regarding Aperture, you'll want to apply the 1.5.6 update from Software Update and be aware of a potentially data-corrupting negative interaction with Time Machine.