Leaving the snorkle in won't give you any ram air effect. There is not nearly enough airflow going under your seat, period. Also, for ram air to work (like in cars or street bikes) the speed the vehicle is travelling at has to be high. Ram air systems that are specifically designed into the vehicle don't start adding power until vehicle speeds are much faster than anyone can ride in the woods. Ever look at the ram air systems on crotch-rockets? They have big openings at the front of the bike. Plus, for ram air to work, it has to pressurize the intake system. If you drill holes in the lid, the system is no longer sealed, and any pressure build-up would just bleed off through the holes.
So, if power is the goal, take out the snorkle, drill holes if you want, or just throw away the lid. But please don't leave the snorkle in thinking that it is going to help you make power.