We have many topics on the subject of using Large Hard drives under OS 9... and many of the Pros and Cons are discussed already...
Please search and read them as they go into more detail...A quick answer would be that if your QS is going to be an "OS 9 Only" G4 then multiple partitions of about 190 GB would be a good game plan (per each 1 TB Drive) since you can perform volume repairs, defrag volumes, and also Boot off the different volumes to perform these tasks in a pure "OS 9 Only" environment. You can also specify whether you want a volume formatted as "Extended" or not (pros and cons also discussed in some other topics)
If you plan to use a large drive as "Storage Only" volume (as you mentioned), then OS 9 will see the 1 TB drive as a single volume, but if the volume gets damaged/corrupted in any way (like a freeze or power failure while writing data), then hopes of fixing the volume (under OS9) may be lost.
In a dual boot environment (with 9 and X), data repairs/drive maintenance will be less of an issue, but please be aware that OS X may write volume info. to an OS 9 shared volume that may generate both file names that are unreadable in 9 and/or volume header errors that OS 9 disk repair utilities cannot fix, that is why some of us (like myself and Mactron), prefer NOT to mix X and 9 on the same G4, they play much nicer on separate units