After a discussion with one of the devs, it turns out at some point in the past (UDK2 or 3) they had an encryption system for sav files alongside other things. They had to remove it because of a few bad experiences in addition of the xBox platform not accepting game encrypted game files (they require everything to be encrypted by the OS). So when it comes to .sav files, we have to secure it ourselves.
Concerning .pak files, ever since Fortnite came out a lot of devs are getting better and better at unpacking those packages. From what I remember, textures, static meshes and animations can be easily retrieved. As of September 2018, it seems the encryption tick box doesn’t actually encrypt the paks meaning they can be accessed ( see [UE4] Lineage 2 Revolution ).