Exactly as you say, there needs to be some hardware in there even for a wired connection. Gone are the days when controllers are simple boxes with buttons on them, the Wii U controller is a complex piece of equipment, and the communciations system would need to deal with the dispaly, touchscreen, various motion sensors, audio, as well as buttons.
Wired and wireless data transmission have significant differences, it is not straightforward to go in and interchange the two. Converting a wired device to wireless is difficult, but possible by using a device specifically designed to mimic a wired connection - for example you can purchase wireless USB hubs, and the rarity of such a device should give you an indicator about the difficulty with which it is achieved (using today's technology). The more complex and higher bandwidth the communications, the more difficult this is to achieve. For example for low bit-rate serial connections, there many devices that will do this - hobbyists would be familiar with XBee, and other serial radio modems; while a wireless HDMI transmitter is even more difficult.
Doing things the other way round is probably even less straightforward, to make a wireless device wired usually involves intercepting the signal somewhere inside the device before the wireless module, sending that over the wire, and re-injecting that signal in the correct part of the device on the other end, all while performing any additional data processing that would have been handled by the wireless module or the nature of the wireless transmission itself.
In short, wired and wireless data transmission are fundamentally different, and other than very simple data transmission, modern high-bandwidth communications that are designed to be either wired, or wireless, cannot be coaxed into the other mode very easily. Therefore any system that is designed for both wired and wireless operation will have two separate subsystems, one to handle wired communications, the other to handle wireless. If the Wii U controller lacks the wired subsystems, there is little chance that you would be able to add one by piggy-backing off the wireless system.
I'm not ruling out what you want to do as impossible, I can imagine a few circumstances where if the Wii U controller does not ship with wired control support but you would still be able to mod it; for example if the Wii U did have the wired subsystem (such as if that functionality was integrated into its microprocessor itself just as USB functionality is built into the processors/SoCs of today's smartphones and tablets) but the few external passive components required were simply not installed, but I would deem this to be unlikely.