From what you say, if the pipe comes from the top cover into the airbox, it is the breather pipe. This takes away any oil mist and gases from the inside of the engine and draws them back into the intake. If you disconnect it, I can honestly say from experience that it will make your car stink. Really stink.
I took mine off and put an ITG breather filter on instead, looked great, but all the oil vapours got drawn into the car through the heater when stopped.
If you had something like the K&N 57i kit, with the filter mounted directly on top of the carb, you could probably direct these gases at it by mounting a breather filter close by.
This wasn't practical with my induction kit, as the filter is mounted away from the carb.
I really wouldn't reccommend taking it off if you are keeping the standard air box.
Pete.
Cinq sporting
http://mysite.freeserve.com/close_to_cracking_up/