Is there a possibility of having a lock added to prefabs that allow it so that when they spawn, on server reboot/wipe, that they're locked?

That's a possibility. I'd like to learn more about this use case. Which entities do you want to lock, and how will people access them if they are locked?

Are you thinking about locking existing map entities? For example, locking hatches, doors and elevators to underground tunnels? If your intention is to block access to monuments, then something possible today is to use the plugin to spawn barricade entities. There are many barricade prefabs that can be used for this purpose. Also, if you are intending to block access to monuments only temporarily, you can use another plugin such as Timed Execute to dynamically execute server commands to enable the relevant profiles only at certain times, without any manual actions.

I was thinking something along the lines of spawning a box as a part of a jump puzzle, and having it locked as a part of that puzzle. You could also spawn a prefab for asthetic purposes and not want players to store things in it. Just a couple things that I came up with. Mine is a bit of both. The prefabs are not intended to be storage, but rather something to stand/jump on. I don't wan't people thinking they have free storage at a monument, though I'd still like the possibility to do that too. I was thinking it would be something like /maspawn <prefab> <keylock/codelock> <code if codelock>. If you just supplied prefab it would work as before. If you used keylock, and it was lockable, it would spawn it with a keylock on it. Etc...

To address that use case, I could probably allow setting a flag on the box which would prevent it from showing the prompt to loot it. I could also allow configuring the capacity of containers, which you could set to 0. That way, you could avoid the minor overhead of the lock entity, while still preventing players from using the box for storage.

I would probably provide these sorts of capabilities via a separate command, since I might want to provide other functions via maspawn in the future, and I want to avoid bloating that command for now.

I think the capacity would cover all cases as we could make it able to be used as storage or not by having a range from 0 to some max value.