the MDDs used a different socket for processors than the Quicksilvers did.
As far as using a G4 for years and years, I suppose it depends on what you do with it. if you only need it for the massive amounts of storage you already have in it, then that makes sense, although the Core1Solo 1.5GHz Mac Mini will far outperform (in CPU/ram tests) any PowerMac G4, ever. (Although yes, that's not really a solution for OS 9, but OS X flies on the intel Macs... so much it's not even funny.)
Plus, you can add loads of storage externally, and it doesn't even have to look awful. One of my projects for later on is to build a large firewire drive enclosure using an older AT case/PSU from a PC, and just piling in a bunch of drives. (That, or a drobo: not sure yet which though.)