Finally, an engineer who'd just completed such a comparison in a wind tunnel noted: Tailgate dropped, the drag coefficient went up by 0.029 (a six-percent gain if the coefficient of drag was a miserable 0.50), and rear lift went up by 0.079. There's your definitive number--dropping the tailgate is more likely to hurt fuel economy, top speed, at-speed handling dynamics, and bed/fastener wear than to help anything. And have you noticed how more and more trucks are coming out with cargo covers and/or tailgate-lip spoilers? The truck business is highly competitive, and manufacturers don't spend a cent more than necessary on parts that aren't worth it--this is especially true when these parts add weight.
The SEMA folks even looked into this tonneau-cover debate, teaming up with SnugTop and Irwindale Speedway to test a similar hypothesis. They took fully broken-in, current-generation V-8 automatic half-tons, got odometers corrected on an independent dyno, then spaced the trucks out around a track to avoid any draft advantage. Each pickup was driven 100 laps (using cruise-control) with and without its cover in place. Note here: Weather conditions weren't constant and the test was done at 45 mph; since aerodynamic drag ramps up with speed, we expect the gains would be better at realistic highway speeds.
The shortbed SuperCrew F-150 was the anomaly, as the short high bed actually lost 0.1 mpg (0.5 percent) with a tonneau cover. The Crew Cab Silverado and Quad Cab Ram, one with a tonneau and one with a cab-high cap, showed much more significant gains of 0.46 mpg and 1.32 mpg (gains of 2.0 and 7.3 percent), and at that speed all three were getting 18-21 mpg without the aids. If the aero improvement were consistent as speed increased, the average gain on the highway could well be better than 10 percent. With the weight of trucks these days, I doubt the added weight of the cap or tonneau would affect acceleration or city economy by a percentage point.
SEMA's working on a more involved version of this test, with multiple trucks and caps, to be performed in a wind tunnel. I predict two things: One, such a test would show that adding a cap or tonneau is much better than dropping the tailgate, and two, there'll still be nonbelievers driving around, durability-testing tailgate hinges.