I'd go with the Full Disk Encryption. You can be sure everything is encrypted that way. Any additional complexity adds ways to mess up and compromise security. Entering the password is a bit cumbersome. But that's part of the deal. I just carry my computer keyboard to my NAS and enter the password each time I need to reboot. Which doesn't happen that often. There also used to be some tutorial somewhere on how to put an SSH server into the initrd so you can enter the password over network.