From Bare's site:
A lot of people ask about the warranty aspect of doing this mod. The bottom line is that it will depend on your dealer and how much of a pain they want to be. Technically they cannot refuse you warranty service based on this mod, but some will because - well because many dealers are a pain in the ass. So they may give you grief over it, but if you call Honda of America (bypassing the dealer) they should make them honor the warranty.
The Magnuson-Moss Warranty Act is a vehicle warranty law - US Code - Title 15, Chapter 50, Sections 2301-2312 states "Legally, a vehicle manufacturer cannot void the warranty on a vehicle due to an aftermarket part unless they can prove that the aftermarket part caused or contributed to the failure in the vehicle." This means that if a dealer tries to void your warranty based on modification to the vehicle then they have to prove (They have to prove, not you) that the problem you're having was caused by the mod you did. Since the desmog (when done properly) cannot cause problems on the bike they would be forced to honor the warranty.