If you are looking to mod a Nintendo 3DS or Nintendo Wii/Wii U, I used these guides:
Everything went smoothly for all devices. It had no effect at all on online functionality. In my experience, there's a lot more homebrew available for the 3DS and Wii than for the Wii U, but I figure that's just down to the install bases for the systems.
Mod your devices and add or restore the functionality you want.