The engine bay on cars is far from sealed. Air can go out the bottom, our out the wheel wells. I wouldn't bother cutting holes in the hood.
Even basjoos'
aerocivic hasn't gotten around to cutting holes in his hood, and I'm pretty sure its one of if not the most aerodynamic car on this forum. He has a full bellypan. I asked him a few years ago if he was worried about engine cooling and airflow through the engine bay, he said there was plenty of airflow out the wheel wells (which he also has covered up).