Does having FileVault enabled affect my ability to see my home folder on the cloned drive?
Regarding FileVault enabled hard drives:
With FileVault enabled via System Preferences>Security, the home folder will be an encrypted disk image. If you clone your startup volume, the resulting clone will also have an encrypted home folder. Unless you boot to the clone you will not be able to see the encrypted folder. You may boot to the clone immediately after the clone script has completed to check the contents of the home folder.
If you wish to restore the contents of the encrypted home folder you will either need to boot to the clone and restore that way, or turn off file vault on your startup drive.
When you turn off FileVault, you will be able to see your encrypted home folder on the clone. It will require your password to access it but you will be able to get to your files without booting to the clone.
If you back up just the FileVaulted home folder and not the entire volume, the encrypted home folder will be visible on the cloned volume and you can access it with just your password.