I replied the following to @cursedd on kind of similar issue few days back. Look into while you think of modifying your bike's air intake:
This was the question:
[I][IMG]https://www.pakwheels.com/forums/images/misc/quote_icon.png[/IMG] Originally Posted by cursedd 
@aximaxim: ok, so it means that it just increases the acceleration of the engine and nothing much.
And i was just thinking why people remove the air box over their filter does it improves the intake of air while its place opposite to the air coming from the front? i am just confuse about the placement of the air intake
[/I]
And this was the reply
Just like a human, an engine breathes......the difference is.....we inhale and exhale from our mouth....whereas the engine inhales from the air intake and exhales from the exhaust. ..................hehehehe........reading what I wrote above made me laugh........khair.............thing is theoritically speaking more air and free flow exhaust will make the engine breathe better thus will increase it power. More air matlab more fuel......matlab bigger bang....matlab more power. Easy and simple to understand.
However the second part of your question is difficult to explain......I'll try anyways.
As far as the original position of the airbox is concerned, the manufacturers are not stupid.......they placed it there for a reason.......and the reason is aerodynamics. The air colliding the frame walls and getting into the airbox underneath the seat inside the frame increases the speed and also make the air cooler than it is outside (something like a "venturi effect"....infact close to it but not exactly). Anyways Faster and cooler air increases the fuel efficiency and power of the engine. People insert turbos to increase the speed of the air and they insert intercoolers to make the air cooler........and they spend alot on it.........We are getting it for free so why mess with it unless you are a modification freak which is not a bad thing.
Inserting a free flow intake infront facing the forward direction of the bike do increase the air speed going into the engine but this air is hotter. Hotter air is less dense and it less effecient to burn the fuel inside the engine, matlab fuel effiency decrea ho jayegi bike ki.
I hope I have made myself clear!