Well technically, the newer games do have protection that can see a modification. But only the game itself will detect this and it will just refuse to run (if you want to know/see more, google for 001 error). No data about this will be sent to Nintendo. But if your modchip is up to date with it's firmware, this new protection is bypassed, so it won't detect your chip and it will play.
And online play with Mario Kart is free, so you're good to go