So what your saying is that something like a k&n kit or equivalent system is also useless?
Yea your not pulling air from the fender anymore, but so what, you've increased the inlet diameter by at least 2 inches if not more. Slightly warmer air or not, I cant see how that's a bad thing. Granted it really hasn't done anything other then make noise- It hasn't hurt performance in any way either.
If you use the K&N drop in filter that replaces the stock filter, you probably get more airflow
capacity, but not necessarily more air flow. The amount of air an engine flows is determined by the volumetric efficiency of the engine (the displacement of the engine affected by factors such as valve timing/lift, intake manifold design, etc.). Basically, an engine is an air pump but the real factor in how much air an engine CAN flow (or needs) is determined not by the air filter but by the engine internals. It is
possible to restrict airflow in the intake system, but Toyota engineers designed the intake system to flow more than a naturally aspirated engine will ever need (I think they even use the same intake system with the supercharger, which probably flows 30% more air than the N/A motor). So, long story short, you could remove the air filter and feed it with a 24" diameter pipe and probably see no difference in HP (and maybe a decrease) since the amount of air NEEDED by the engine is less than the factory intake system flows now.
If you use the complete K&N intake system (57-9015-1) you might gain a little. They claim 9+ HP, but anyone who has run a dyno will tell you that you can see almost that much difference between pulls with no changes. There is a trick that cold air kit manufacturers do that can make a little power, but it's generally frowned upon by people who tune cars. They increase the size of the MAF meter portion of the intake tube which results in a leaner mixture (the MAF meter thinks it's flowing less air than it is so at WOT the mixture is leaner). It runs okay at part throttle because the ECM richens the mixture since the O2 sensors tell it that it's lean. Most engines will make a little more power at WOT by leaning them out from factory A/F (which is probably where the K&N increase comes from, if it exists at all). The K&N complete system also takes in cold air from the fender well.
Bringing in warm engine bay air with the deck plate mod probably will reduce power due to two factors. First, warmer air is less dense, therefore the air and fuel mixture has less mass, which means it will make less power (why do you think they sell 'cold air kits'?). The second reason is that the ECM will pull timing and richen the mixture as the IAT sensor detects the warmer air, to protect the engine. Both of these will reduce torque and power. Granted the intake air temp will not be what you would see with a supercharger, but in traffic or at slow speeds it will probably increase the air temp by at least 30-40 degress (more on cooler days), which means the ECM probably will pull at least 2 - 4 degrees of timing.
Removing the resonator will probably increase the amount of turbulence and standing waves (pulsations) in the intake tube and may interfere with the MAF accuracy, resulting in worse part-throttle performance (less torque, worse fuel economy while cruising). That's typically why manufacturers use Helmholtz resonators. You see this problem in engines with centrifugal superchargers if the blowoff valve returns air too close to the MAF.
These mods probably don't hurt power or economy much but they almost certainly don't gain any power or economy. The main concern in an off-road vehicle is clean air. Grit and dirt will kill an engine quickly and the factory-style paper filters do a much better job of filtering than cotton or foam filters. I'll vote for longevity over noise (or even a little more power) any day.
(Sorry for the dissertation!)