Solution: It was the extra USB hub and devices (printers, scanner, etc.) Unplugged the extras, leaving only the keyboard in one usb port and the mouse plugged to the keyboard. Drives now visible and OS 9 shuts down properly. I don't have a clue why this happens but I have tried it on two different G4s and it is a consistent bug.
[robg adds: Without more detail on the devices and the hub in use, it's hard to say for sure, but I'd bet this was caused by the hub more than the devices. There were many reports of similar problems with certain USB hubs in 10.0 and 10.1, but this is the first I've heard with Jaguar. If you're having a tough to diagnose installation problem, try removing all the non-stock parts from the machine in question and see if the problem goes away...]

