If you ever go to the dealer for repair work under the warranty, in order to deny your warranty claim the dealer would have to show that your specific modification caused the damage that is in need of repair.
Slightly off topic, but I would consider going with brighter aftermarket halogens instead of aftermarket HIDs. The downside is that the brighter aftermarket halogens burn out faster than the OEM halogens. I put on the Phillips X-Treme Power Bulbs. They are extremely bright. Seemingly 80% brighter than standard halogens. But my bet is that they only have about 25% to 50% of the life expectancy of the standard OEM halogens.
I hope your HID kit has proper projectors or is a retro-fit, otherwise you're gonna blind on-coming traffic.
It shouldn't? It can't. By law. There is nothing that you can do to the car that voids the entire warranty. If you replace a light bulb and the wipers stop working - Toyota would have to prove that the light bulb caused the wipers to fail in order to deny the warranty claim. It still amazes me that the general public has been so scared into not wanting to touch anything for fear of voiding the warranty.