The snorkel is there to help keep water out. If you're going to do a lot of water riding, you may want to leave it. If you, instead, want to increase performance, remove it and rejet.
If you remove, put a filter on the breather tube - it has little airflow, what's there is usually out, but a filter will keep dirt from migrating in.
'01 660 Raptor, Burgard +2+1 arms, YFZ Shocks, LSR anti-vibe, CTR pipe, jetted, K&N
'01 Polaris Scrambler 400, K&N
'02 Honda 400ex, Big Gun pipe, jetted, K&N, Lonestar +2 A-arms, Lonestar anti-vibe
'02 Honda 400ex, DiamondJ +3 A-arm widener, Lonestar anti-vibe