I don't see any reason why you wouldn't theoretically be able to do this as long as everything is setup properly (SCSI id's, SCSI terminates etc). I do remember hearing something about avoiding having FAT32 drives mounted by both the E-mu and the PC at the same time as this could cause data loss etc. The 18 gig issue is only localized to E-mu formatted HD's but FAT32's limit is unknown to me if it exists at all. If you need a detailed summary as to why there is an 18 gig limit of E-mu disks I am sure there are posts within this forum addressing this issue... I'm just lazy.
I have not done any bench mark test but I seem to recall E-mu formatted disks are faster than FAT32 but that really isn't a huge issue. With an E-mu formatted disk you could make E-mu formatted CD's but other than that I think, if you can, FAT32 is definitely a better option in terms of PC/Mac visibility and for backing up/sharing banks.