Yes, they will replace it. It doesn't matter if the pixel is off to the side or in the corner. If it bugs you, they'll replace it. Trust me, I've talked to a lot of people about it.

I own Mario 64 DS, WarioWare Touched and the Metroid Hunters demo. I use the thumb-strap for Mario and Metroid and the stylus for WarioWare. The thumb-strap is best for more intense, action-based games like Mario because it allows you to hold the system with both hands. The stylus is better for touchscreen-only games like WarioWare because you get more precise control and you don't need to use your other hand to press the buttons.

By the way, I'd highly recommend picking up WarioWare. One of the weirdest, most addictive things I've ever played.