There's quite a few people who have modified their airboxes. I have cut out the bottom of my airbox - the "horn" that hangs down at the bottom, and that's it. Just don't cut too much out so you end up with a chance for moisture to get in. Keep your cuts to the lowest portion of the airbox, where its the most protected fom the elements by the frame.
One thing to keep in mind, is that if you increase airflow to the motor, you may need to install a fuel controller to add more fuel. Also, you may need to adjust the factory fuel settings via the control panel.