SetProcess will toggle the _Process function, and SetPhysicsProcess wil disable the _PhysicsProcess.
Which one is better depends ENTIRELY on how your cure is structured and which function you use to process things. Since if you only do things in _PhysicsProcess and _Process is not even overridden, then SetProcess will do nothing, as _PhysicsProcess will continue to execute your logic inside it.
And as for which way to disable or enable it, as far as I know it depends on how you structure your nodes. The second way has a bit more control.