There may be some truth to the ram air impacting performance. Last year while I was testing water wetter vs eth glycol for engine temperature performance I came across an effect that I noticed - that clean ram air impacts engine temperature significantly (well anywhere from 10-15 degrees). Try this sometime - go and get the engine nice and warm and go on the highway. Drive behind someone on the highway for awhile and note the engine temp. Drive in a clear lane at the same gear and speed and note the speed. It will surprise you. I don't have the exact numbers from last year, but off the top of my head for eth glycol (regular coolant) - in 3rd gear around 70mph, if you were running behind a car and there wasn't good ram air flow, you would be around 205F. If you had a clear lane with good ram air at that speed/gear the temp would drop to around 190-195. A good 10 degree difference. Water wetter would drop it another 7-8 degrees as well. ..
Obviously this depends upon ambient air, etc, etc. But there was a noticeable difference when you had nice clean air vs say turbulent/non ram air. I didn't expect 10 degrees but sometimes it seemed greater than that . So - I'm not saying as I have no idea how that 10+ degree of engine temp will impact HP/torque in any given rpm range, but there is a difference in temp based on ram air. Go ahead and ride and try it out.
I would suspect disrupted aero effects, (i.e. turbulence) as the primary cause of the loss of cooling efficiency rather than intake ram air effects. Dead low pressure zones contribute to all kinds of performance issues, from overheating to lack of downforce, or excessive lift, etc.
Laminar intake air flow does indeed affect performance positively.
High performance intake manifold design normally incorporates bell-shaped mouths on the runners which are visible on individual throttle body (itb) set ups to improve flow and reduce "turbulence". The nice thing is you can do searches on patents and read all the "secret" information about these designs. Shh, don't tell anyone though.
I personally run a sheet metal intake manifold that uses them and a velocity stack on my intake pipe (car) which gives good gains with high cfm. Gains are more noticeable on turbo applications due to the huge potential to raise VE. Pressurizing the intake air, say with fans, or a centrifugal supercharger, turbo, etc, will improve performance with the right tuning.
Clean air optimizes the potential, consistency, and efficiency of many parts of the bike, including the suspension system. Controlling the air flow over and through the bike (in this case) is extremely important to maintain the efficiency of the cooling system. Drag is always the enemy, but some design trade-offs are necessary in order to cool the bike properly.
Drafting is great for saving fuel though. Just watch out for potholes and delaminating tires when drafting rigs.