I know all of that, there's no logic to ban an user with CFW, and If I mod my 3DS, I own my risk
Honestly, Nintendo is joking with us, because they said that the 11.5 (or some other update) will be the last support for 3DS, btw they study every strategies to block this modding after that.
I want to say that they release a software to make a "trap". Who is supsected and didn't update, will get banned. (because they're worried about updating). Who update might got a "timerbomb" inside its 3DS. We don't know anything, just suppose!
But the 11.6 includes a new Friend List source code, for examples. That's different between 11.4-5, they may insert something in the update code..