It means all online Nintendo service will be unavailable for the 3DS and the Wii U.
So, the eShop and online game servers will shut down. You won’t be able to purchase any game digitally, and online multiplayer in games will not work. Neither DownloadPlay, probably, but I’m maybe wrong there.
Homebrew, fortunatelly is not provided through any of these channels and they are not dependent on any online Nintendo service.