Standard airbox as Honda intended gives a solid 40~45hp as Honda and the Japanese government intended.
Modifying the standard airbox gives some more hp and adds some more induction noise. There really isn't anything lost by doing this, but you will need to re-jet for the increased airflow at the top. We went from stock #128 mains (MC21) up to #142's. This is a good modification and is pretty much free apart from the cost of the jets.
Taking off the airbox adds loads of noise, but not a huge power increase. It would seem that the major change here is doing away with the rubber 'velocity stacks' that connect the airbox to the carbs. These would help the bottom end power by keeping intake velocity high at low rpm, but aren't particularly good for absolute top end power. Had good results with keeping the airbox, but cutting down the stacks level with the airbox and smoothing them off a tad. Midrange is good, with extra top end mojo.