A few tips:
1) A "nearly full" hard drive will perform significantly slower than a "nearly empty" hard drive +even+ if there is no fragmentation. There are several reasons for this but if you check benchmark performance studies for drive after drive you'll find that you can generalize by stated that a full drive will be only about half as fast as a new (near-empty) drive ... and that's with no fragmentation at all.
For this reason I try to keep my "working" hard drives from becoming much more than about half full. I will let "archive" drives fill up (since I don't need quick performance for them) but I keep "working" drives down to a capacity that still guarantees snappy performance.
2) If your drive never becomes more full than about 80%, you will +never+ need to defragment it. The Mac's HFS+ filesystem strongly resists fragmentation if at all possible. It only fragments things when it gets desperate for space. This isn't to say you'll never have any fragmentation... you will, but it'll be so extremely minimal that you wont see any measurable performance gain by defragmenting (defragmenting will become a waste of time and needless wear and tear on the drive. Defragmenting causes drives to heat up substantially and can be brutal to hard drive life expectancy.)
3) In "System Preferences" -> "Energy Saver", there's an option to "Put the hard disk(s) to sleep when possible." You can turn this _off_ (no checkmark in the box) to improve performance. With this said, my box +is+ checked (my drives will sleep) and I have absolutely no problem with Aperture 3 (I _do_ have problems with Final Cut Studio and when I use that I have to un-check the box or I'll get a lot of beach-balling.)
In general, I find that Aperture 3 is pretty rock solid and very fast, but it really helps to know a little about how it's working under the covers.