I would suppose that you don't have to change pads, especially since you usually have to do a bit of shimming to get them lined up just right, but I don't know why you wouldn't- it would make sense to use the same product on both sides, and if one wears the other should be too.
I agree with you about the hydraulic principles- if you were to find or build a dual circuit master for a motorcycle, it would be valved for even operation on both circuits, and the brakes would come on evenly as they do on a single circuit.