I have observed (both first hand and anecdotally) that this is a very common problem with MDD G4s under OS 9, and that people have come up with solutions like replacing the fans with quieter versions (probably not a terrible idea *anyway*), downgrading from a dual to a single CPU card, and, the most obvious, running Mac OS X exclusively (and using Classic if running Mac OS X =< 10.4.11) and using the CHUD tools.
With all these workarounds, I've noticed that nobody has even considered an attempt at duplicating OS X's control mechanism in an OS 9 environment.
It seems like, at the very least, an OpenFirmware hack could be devised that would at least allow the fans to run more slowly, but a more flexible approach would be to somehow write an extension and/or control panel that would exert the same kind of control over the fans as OS X's AppleFan.kext, which would probably be ideal. I've wondered why Apple itself wouldn't have done something similar, but it was probably due to the fact that the MDD was released when OS X was taking over (and OS 9 was on its way out), so it's quite understandable. Likewise, it's understandable that nobody else would've cared as much since the Quicksilver, the MDD's immediate predecessor, was perfectly adequate under OS 9, so there was little reason to bother trying to run it flawlessly on an MDD, despite the fact that the MDD was an OS 9 bootable machine (except the FW800, of course).
So, is anyone willing to take on this project? I'd like to do it myself, but I don't know enough yet