This question has been asked alot of time. I think on the old board there was a long thread about it. check archives and you might find stuff there. I think the final consensus was that if Hyundai can prove your aftermarket part caused the factory part to break or malfunction, then you pay. example:adding a cold air intake wont cause a rear wheel bearing to go out, in other words just adding an aftermarket part will not void the warranty.
On the other hand, if you put in an aftermarket cam, and bend the valves, and Hyundai can prove the cam did it, bend over.
Ok, this is basically how it works boys and girls,
The Magnuson-Moss Warranty Act was passed in order to protect those who have modified their cars, as well as car companies. The concept is pretty much this:
If the dealership can prove beyond a reasonable doubt that your aftermarket product had a direct relationship to the problem which occurred, they can void your warrenty on the part/system and refuse to honor the warrenty.
However, if you have aftermarket parts that are unrelated completely to the problem at hand, the dealership is required by law to honor the warrenty, and service the vehicle.
Also, if you get work done by a shop, such as an audio install with a high wattage or amperage draw(electrical system), or an aftermarket muffler system (engine/exhaust), I reccomend that you keep your receipts. Most dealerships will just say "gah, fine" and do the work if you come in prepared with all your information, and can prove to them that the aftermarket work is done by a professional.
oh, if I made any mistakes, pm me and I'll edit this.
The above is my interpretation of the Magnuson-Moss Warranty Act.