They will be more manageable if they are formatted ext4 and mounted via fstab. The OS that is local to the machine (in this case Ubuntu) should be the determining factor. The remote hosts ( windows computers and the mac) will still work the same as now since you are using Samba (CIFS) to share files and directories.
The setup of the shares in smb.conf will change as the paths to the files will change. Everything else is the same. You should be able to manage remote users better with these re-formatted drives.
Thank you very much for the info! Also sorry for my slow reply, it's midterm season :-/