I'm not sure about a NNID being different as club Nintendo but its different for the Wii U and the 3DS. I emailed them about it and everything and they made it very clear I had to access the net from my gamepad and create some Nintendo ID which I then log in to club nintendo and it registers my 160 points. It's impossible to do without connecting to the internet via gamepad.
I can definitely confirm you need to use the Wii U itself for the Nintendo ID (which is the NNID I keep refering too.) I had to do that on my 3DS to be able to use the online store. Also, it used to be that your NNID was different between 3DS and Wii U, but they've since changed that. You can use the same NNID for both.
That being said, I created my NNID
after i created my club nintendo account and registered my 3DS with Club Nintendo. All I really did was link my NNID to my Club Nintendo account. They're completely different log in information so I know they're separate.
If nothing else, you should go to club.nintendo.com, create an account and register your games. They can give you coins too. While you're there, you might as well try to register your Wii U serial #.