You run the risk of voiding the manufacturers warranty with any aftermarket product however if you run into an issue, just reinstall the stock intake before going into the dealership. You're warranty cannot be voided unless they can prove the intake caused the problem. For instance, if you have problem with your brakes and you have an aftermarket intake, your warranty cannot be voided for that particular part. It only voids the warranty for the stock intake and any problems the dealership can prove were caused by the installed part.
Some dealerships may refuse to work on your car with aftermarket parts (knock on wood, I have been lucky and not run into this problem with Lexus). If you're concerned about this, find out what local dealerships are "mod friendly" and which are sticklers about aftermarket parts.