i really don't see how it could, unless you went in for a warranty claim about your speakers not working and they discovered it was because you wired it up wrong or fried something. but mechanically, i don't think you have to worry about any warranty issues.
let me know how bad it rattles though...i have a sub I want to install but i'm holding off for that reason
Warranty issues are not a yes/no deal. But as you go down the line (factory install - port install - dealer install - aftermarket shop install - self install) the more likely problems will not be covered under warranty.