OS9 has a 128GB limit. You can defeat that with InTech's HiCap driver though. OS X will see more than 250GB, particularly if you are using a SATA PCI card.
My Quicksilver has two 500GB SATA drives and two 160GB IDE drives that I RAIDed together to make one 260GB RAID drive.
The MDD machines (and some of the Quicksilvers too) have no size limit on the ATA controller - you'll be able to use the full space of the drives without any problems.
There is a limit in OS 9 that will prevent it from booting from a disk that is larger than 200GB. If your disk is larger, it should be partitioned. OS 9 can see and use volumes larger than 200GB. Just booting from them is the problem.