I predicted they would have stopped this summer, but I was wrong. 3DS and Wii U online play are still going strong. I play Splatoon 1 and Ultra Moon online on a regular basis.
The Pokemon "Global Link" got shut down, but that was pretty much just a web interface. All other online features still work fine. I expect we would still have the official Nintendo WFC (for DS and Wii) if that network wasn't beyond Nintendo's control.
You won't be banned for installing any CIAs. If you were to install a fake ticket and try redownloading the game from the eShop, then you could get in trouble.