I would not drill holes in the stock air box as the air box can flow more than enough air. On the AU/EU/UK bikes Honda installed a rubber plug blocking 2/3 of the opening. With only 1/3 open it flowed enough for the engine so removing the rubber plug and switching to a K&N filter will flow more than enough air from a performance point of view.
Changing the air filter for looks or to stop it hitting your leg are another matter.