YES, I have wondered about getting OS 9 booting on a newer MDD myself. One could simply flash it with firmware from an older MDD and "see what happens"! I have one of these MDDs myself but it's still too useful to experiment on.
From what I understand, these are the differences between them:
USB controller is USB 2.0 (though not implemented by Apple!! Runs only at 1.1)
Airport Extreme vs. normal AirPort
Bluetooth expansion port vs. no bluetooth
FireWire 800 vs FireWire 400 only
The logic boards appear nearly identical otherwise.
Also of note is that the Apple Hardware Test disc for the newer MDD boots the Mac using some conglomeration that involves an OS 9 System File and some open firmware script. If memory serves, the script is a hidden file on the disc. There is no OS X on this disc and it boots, so it's definitely something worth poking at. It's non-destructive if you play with it and keep re-burning a CD-RW.
From what I understand, these are the differences between them:
USB controller is USB 2.0 (though not implemented by Apple!! Runs only at 1.1)
Airport Extreme vs. normal AirPort
Bluetooth expansion port vs. no bluetooth
FireWire 800 vs FireWire 400 only
The logic boards appear nearly identical otherwise.
Also of note is that the Apple Hardware Test disc for the newer MDD boots the Mac using some conglomeration that involves an OS 9 System File and some open firmware script. If memory serves, the script is a hidden file on the disc. There is no OS X on this disc and it boots, so it's definitely something worth poking at. It's non-destructive if you play with it and keep re-burning a CD-RW.