Well, on larger vessels, there's a Soul Savior Pod that keeps your backup and it's usually very well protected and ejected in the case of ship destruction. Now, there's nothing saying we can't keep back-ups anywhere and everywhere; but when your ship doesn't have a Soul Savior Pod, you've got to get yourself backed up wherever you can, right?
Leo Station isn't the only place our backups could be reliably kept. It's just the logical place they would be kept because it's our Fleet HQ. Besides, there's really no reliable place a backup can be kept. Stuff happens. Data gets lost or damaged. What's the difference if it's on a star fortress or in the Imperial Palace? Even Yamatai was attacked at the end of the last war with the hamburger squids. There's little to be done about it in the end. Even Soul Savior Pods get found fried (one just did) on some planetside in the middle of nowhere-space.
Where do you think our back-ups should be kept? Or are you just thinking maybe we should make redundant copies of our souls?