I examined the warranty a bit closer today and I can't find anything that would indicate that rooting voids your warranty.
First of all, take a gander for yourself here
Notice the warranty only covers the standard "defects in workmanship or material" and that in several places they specifically state that the warranty only covers the hardware. In on paragraph, they state specifically that it doesn't cover the software.
The have the standard disclaimers about damage or malfunctions caused by abuse, neglect, Vogon poetry, etc. not being covered, but nowhere does it say that modifying or configuring your NC automatically
voids your warranty. If such modifications cause
the damage or malfunction, that's a different story.
So they could say that overclocking your CPU voids your warranty but only if it's the CPU that is damaged, however. If you overclock your CPU, they would have a hard time demonstrating that that was the reason why you have 18 dead pixels.
Then again B&N is a big corporation with nearly unlimited resources and you might lose if it ever came down to a fight. But there are a number of laws in place to protect us, the little guys. It also would be worthwhile to investigate whether your state has extra automatic warranty coverages.
That said, you'd probably be safe to factory reset your NC before trying to return it or get it serviced under warranty - especially since you won't get that specific unit back.
Or you could shell out the $55 for the 2-year extended warranty that covers everything
Remember to have your pet Nook nootered!