Thing is, Nintendo could very easily implement a list of all the console IDs, in the same way that computer software stores their product keys on a server and then keeps track of them to see if one has already been used, or if the key doesn't match any of the keys on the server in which would then reject it if the user tried to put in a random letters and numbers as a product key.
It's either that, or Nintendo is doing a Friend Code ban, in which bans the Friend Code that is registered on the Nintendo 3DS. But I highly doubt it though, since a console ID is more than likely, since they're used on both 3DS and Wii U in the hardware SOC. I'd assume that a console ID is actually different from a serial number, I would assume it's a huge line of hexadecimal values (probably two or three lines) stored inside the SOC.
So even if we did spoof the serial number or console ID in the SOC, Nintendo would learn from it and upgrade the software on their server to include the whole list of console IDs from what they've manufactured (and of course, who wouldn't keep a list of all the IDs of everything that is manufactured).
Warranty is already voided as soon as you use "unauthorised" software.