It's always best to have a good relationship and understanding between you and your service department. Just because we have the law on our side doesn't mean we can afford to be jerks about it. Basically, when we modify the car, we're deviating from Nissan's well laid development work. They can no longer guarantee functionality for the warranty duration. However, as most aftermarket parts barely change anything [except crazy stuff like turbo kits], the
Magnuson-Moss Act says Nissan has to honor their warranty for breakage or failure for all items that they put on the car that failed themselves. If aftermarket parts caused the failure, then we're SOL and have to foot the bill to fix it.
Since there are so many idiots running service departments out there, it's really easy for an owner of a lightly modded car to pull up with an honest warranty issue and get "black flagged" by the dealership system where all warranty claims are voided. This is most likely a failure to understand the root cause of the problem. A competent mechanic that has excellent knowledge of vehicle functionality will be able to easily deduce root cause, and thus if the warranty is applicable or voided. So basically, find a good mechanic and service writer that understand what you've done to the car and how it may or may not impact certain systems.
Back to the OPs question, it would be very easy for a service department to not honor warranty work if you, for example:
*broke a drive axle at a drag-strip using slicks
*broke any drivetrain part after adding power-adding devices [even things like cams, exhausts, intakes, unless you can prove those parts did not add any power]
*broke suspension pieces after installing solid bushings, or even coilovers
Obviously if your NAV system failed, it has nothing to do with your new exhaust or coilovers, so there is no logical reason for unrelated components to cause a problem and the dealership giving you hassle.
Cheers,
Ryan