the purpose behind having secondary throttle plates is not for emissions. they control the amount of air flow entering the engine based on load, atmospheric conditions, and engine speed.
by keeping the secondary throttle plates closed at lower engine speeds you are making the air enter the engine at a higher speed than it would be if the intake tract was wide open.
higher air (speed)velocity = more torque and power at low-mid engine speeds. which is where your bike gets all its wheelie power.
they open up fully when approaching peak hp so the air volume(quantity) is increased.
kind of like turning the water hose on full blast and putting your thumb over the end. the water is coming out at a higher speed. this is velocity. when you remove your thumb you get a higher volume of water, but it's moving slower.
more velocity makes higher low end/mid range power. (torque/wheelie power)
more volume makes higher top end and peak power.
removing the secondary throttle plates on a stock engine with no other mods isnt giving your engine any more power or bringing peak power on sooner. its slowing the air speed entering the engine down thus having a negative affect on low end output.
having the STP in is not going to affect peak hp anyways because the bike can only flow so much volume in the first place.
its all about intake tuning.
research variable length intake manifold.
THIS is the same concept.
maybe if you were to tune the bike to compensate for your changes could you see an improvement. and of course changing displacement, cams or the way the head flows would also affect this. but that still doesnt change the fact that you dont need large volume of air at lower engine speeds.
AGAIN, if i am wrong, please correct me!