Why would the DSi and Wii get an update? It would be pointless. The Nintendo CWF has been shut down for over a year now, and those consoles are basically "dead". Nintendo even releases DS and Wii games on the Wii U...
For the 3DS, honestly, it's not a problem. You always need to confirm you want to update your system, and a lot of times, so if you update, it's that you want it. And even if TubeHax itself is dead, the DNS itself is still usable at the moment, and it blocks access to Nintendo Servers. So...
And they can't patch SmashHax nor OOT3Dhax. It's "easy" to update a download app, but they can't burn those patches into your cartridge. The worst thing that can happen is that they "patch" the new prints of the game, but the ones you keep in your shelf will be forever an entrypoint.
As for the Wii U... Yes, it is a bit more problematic. Guess I will just have to disconnect it from the Internet now.