I too have been considering getting a 360 at some point, based on my studies there are a few things to be concerned about.
1. Service history is important, some time gaps in history are probably acceptable as long the last service was very recently done by a reputable shop, with records.
2. For 1999 through 2001 cars...the Cam Variators should have been upgraded.
3. Watch for evidence of frame cracking issues around the engine and rear suspension.
4. A repaint of the nose is common and doesn't detract from the car if done right.
5. I've heard that sometimes there are problems with the exhaust headers.
6. Get a good PPI by an experienced technician prior to purchase.
Cars after 2002 have all these issues corrected. But any previous cars with these issues fixed is just as good as a later car. The 1999 year is probably the lightest and fastest of all 360s, the later cars got weighted down with additional emissions and safety stuff.
The reason for dropping values is OBVIOUSLY the current economy, but also because they made so many cars, somewhere around 16,000. This is the highest single model production every by Ferrari. So they aren't rare at all.
I prefere a 6-speed manual car, because I like more interaction with the car and an enhanced driving experience. Another benefit of manuals is fewer gizmos to go bad. I've heard that F-1 tranmission cars tend to have shorter clutch life and manuals. But there are owners how there who say this isn't true.
Read through the 360 Buyer's Guide on this website for more information.