I'm not as knowledgeable as some folks here, but I wouldn't suggest it.
First of all, it will throw off the back-pressure balance, and you'll loose power unless you re-jet and/or run pods. There needs to be a good balance between intake and exhaust, if either of those are out of whack, you'll experience power loss.
Running headers may also put your valves at risk. They'll get too hot and burn if you run this way for too long. It's okay to do this at the track because the engines get rebuilt frequently, but for everyday use straight headers could do permanent damage to your engine.
I don't have any other good alternatives to suggest, but I definitely would avoid just cutting 'em off.