As far as I'm aware, there no problem in running Zimbra on a JFS file system (I prefer xfs myself

). The reason we recommend ext3 is because it's the one we test on and it's the most commonly used file system tec, etc....
If you're happy with the facilities that JFS provides for backup and maintenance then feel free to use it. If you'd like a definitive answer then please check with support but I wouldn't see any problems.