Having been involved in modding circles, I am very familiar with Nissan owners fed up with dealers not honoring the factory warranty due to aftermarket modifications. The modders like to quote the Magnussen Moss warranty act as reasons to why the dealer should service modded cars which are still under warranty.
I believe the Magnussen Moss act says that the dealer cannot refuse to service a vehicle under warranty unless they can prove the aftermarket part caused the damage. With aftermarket, I believe this applies to OEM type aftermarket parts - i.e. replacement parts, not performance parts. I can imagine why the dealer would refuse to fix an overheated engine if it was modded to be more powerful with exhaust or intake mods. However, the dealer cannot refuse warranty service for a part which is defective and independent of a modified part. For example, if you modified your suspension and the radio stops working, they cannot refuse service. But if you develop a shimmy and your car is lowered, well thats out of pocket expenses for you.
My experience with modded parts at Nissan dealers have been rather neutral. They have never refused service, but on occasion some oil change guy at the dealership will pretend he knows how all the mods on my 97 Maxima work and give me "suggestions." When I took my car in for a courtesy inspection during "Nissan maintenance month" they removed my lower airduct and resonator because the tech claimed I did not need it since I had a cone filter intake. From all I read on Maxima.org, removing the resonator did NOTHING to improve performance and even though the dealership gave me back the stock parts, they did not give me back the fastening screws so I can never put the resonator back on if I wanted to.