Yeah, sure it's wasted energy, but I think that it's negligible compared to the vertical shock absorption being done by the tire/fork/frame/rider with a softer tire in light of the differences in propelling forward. The more I think about it, I think you are right that you've got to measure this in terms of power output by the rider instead of just rolling resistance numbers for a tire since travel in the vertical direction would be hard to measure. The fewer watts it takes to go X mph over different terrain with different pressures under the same wind conditions would mean that the tire setup is "faster" because the ride would be more efficient.
I'm not sure how many watts we'd be talking, though. I would guess not that many, based on my assumption that this topic eventually boils down to personal preference for comfort, the road "feel" for a given tire, and the odds of getting a pinch flat due to ease of compressing the tire.