I personally use NIP 78 to store user preferences, which are signed events on relays. If you're storing them on your server, I wouldn't bother signing them, since they're verified by your server. Unnecessary signatures/encryption creates more requests for user signers, which is UX friction.
In my use-case I’m storing a push token associated with the users pub key so the user can receive push notifications for events that happen when they’re not in the app. I just read nip-78 but it seems not quite right for this particular use-case as I, on the server side, need to query my db for a set of users pubkeys to get their push token to send notifications?