Yes, OS 3.9 can handle hard drives up to 128 TB (IIRC).
But when you turn the machine on, 3.9's enhancements to the Kickstart ROM are not enabled yet (they have to be loaded from disk). Therefore, your boot partition should be below the 4GB barrier. All other partitions can be as big as you want.
Just remember not to access any partitions beyond the 4GB barrier without OS 3.9 - if your boot partition gets corrupted, boot from the Emergency disk / CD instead.
