Gutting the airbox usually involves cutting out anything that isn't necessary, but is put in there to cut down on noise, etc. The idea is that by doing that, the air passes through more easily, and you get more power.
I looked in my airbox for my '89, and I didn't see much that could come out. I think the newer ones have more baffles and obstruction (more room for improvement).
Some people have also managed to gut their airbox and install a small K&N cone filter, at least on GP'*. That would give the maximum benefit, but i'm not sure if or how that works on a bonnie. I can't afford one right now, so I didn't look into it anymore.