So I want to create a new NNID account on my 3DS (because long story short my NNID region is set to mexico even though I'm in the US). However, I bought a lot of things on this account and I'm not sure if I can create a new NNID (or use my Wii U account) and still keep the games I purchased. I really hate having my region settings in a different location. I really don't want to buy hundreds of dollars worth of games again. Or at least can someone explain the formatting thing? I heard you can redownload the games even without the account but I don't know how that works.
No, you will lose the games or be forced to transfer them to another system.
Games are tied to both the system and the NNID. The 3DS only supports one NNID to be linked to it at a time, unlike the Wii U which allows 12. The only way to unlink a NNID from a 3DS outside of a system transfer is to format the system. If you link a new NNID after that, then you will not be able to redownload the games.
Your best chance is to contact nintendo's support and see if they will help you out.