OS X 10.6 uses FileVault 1 technology, which just encrypts the user’s home folder as a sparsebundle. OS X 10.7-10.9 uses FileVault 2 technology, which encrypts the entire boot volume. Both versions of FileVault should only be enabled when the Mac has extremely sensitive data on it, and there is a risk that the Mac could be stolen. 99.9% of Mac users do not need FileVault, and turning it on will cause a performance hit on the Mac due to all the encryption/decryption routines being processed in the background. Having FileVault enabled also complicates usually easy troubleshooting steps.
If you are migrating user data from OS X 10.6 to a new Mac, and the OS X 10.6 Mac has FileVault enabled, it should be disabled first before the migration. After the user data has been migrated, FileVault can be enabled on the new Mac at the user’s digression.
Although it’s possible, it’s not recommended to migrate user data from OS X 10.6 to a new Mac if FileVault has been enabled on the OS X 10.6 Mac. What happens in this scenario is the encrypted home folder will be moved over, and OS X 10.7-10.9 will use a backward compatible mechanism to access the older FileVault 1 technology. This puts the Mac in an extremely non-standard state, where FileVault is partially enabled but not showing as turned on… plus there’s no mechanism for straightening out this situation.
Furthermore, All Covered Chicago has recently discovered that if you migrate an old FileVault 1 user folder to a new Mac, and you are logged in as using that FileVault enabled user account, the associated sparsebundle folder is not protected by the OS. You can actually put this sparsebundle folder in the trash, and empty the trash, all while being logged in as the user! This of course creates a situation of complete data loss once the OS figures out the sparsebundle is gone.
So long story short… don’t migrate FileVault enabled home folders from OS X 10.6, and if you do be careful not to accidentally delete the copied sparsebundle folders.