See my post above yours regarding my experience in a home-made FusionDrive. I too was experiencing the "lag" between when an app launched, and when it was usable, due to the external HDD spinning down or just the latency in it being an external drive. Even though my FD is a hybrid internal/external, the important-to-have files have all been migrated to the SSD so I get no delay when launching apps.
Another possible solution is to keep the drive from spinning down. I have used an applet called "Keep Drive Spinning", which goes out to each drive you specify and "touches it" by writing to it once a minute. This keeps it from ever spinning down, as some drives' firmware over-ride your energy management preferences.
Also wanted to add - my experience with Aperture has been that with 6GB of RAM, the most updates to Aperture 3, and then going to Mountain Lion (with having the Library on the SSD and my masters referenced on a FW800 drive) has been my best experience ever. It is pretty fast with minimal lag. I only experience lag when using lots of brushes. My page outs have been reduced dramatically. I am processing D300 RAW files (12MB - 14MB each).