Per the Magnuson-Moss Warranty Act, any modification that you make to your bike does not, in and of itself, void the warranty. However, if you suffer damage that can be directly tied to said modification, then the company can deny the claim.
For example: I have a gutted head pipe. I submitted a warranty claim for my front fender rusting. Front fender was covered, no questions asked. There was no way that the gutted cat could cause the fender to rust.
It also depends on your dealer. If they are "mod friendly", then when you file the claim they will not mention the mods. Also, the dealer would have to know that the mod was there in the first place. So, if you take your bike in to have something fixed that is not exhaust related, why would they even have a reason to look in the tailpipe?