Oh, there is a cunning way to do that.
In Drive Setup, select the disk and go to "Customize Volumes..."
Then select the partition you don't want to mount.
Deselect "Automount on startup" and it wont appear on boot. You can manually mount it using various utilities including Drive Setup, and unmount it again by dragging the disk to the Trash / Wastebasket.
Or sorry, do you still want it to be mounted, just hidden? That is a strange thing to do. It isn't really how Classic Mac OS works. The desktop is where mounted disks are. Bodge I can think of is to set a clear / empty icon and a null character name, but you'll still get a small vertical white bar for the name.