The Lambda probe, should you have one, says that removing the snorkels reduces airflow. Or, in other words, reduces power output. Holes in the airbox cover on my bike had no influence at all, besides that the box was onerously loud.
Basically it depends on your acception of the bike. If you find it better pulling or performing with those modifications then they are good for you and the bike. Otherwise go back to OEM configuration. It's not a bad one either.
hubert