Users of hacked/jailbroken 3DS consoles have unfortunately found them on the wrong end of the Nintendo ban-hammer recently. Many users of custom 3DS firmware (also known as CFW). Have been banned from any 3DS online services, as stated by Kotaku.
I was first made aware of the news through the /r/3dshacks subreddit. There is megathread/faq regarding the issue here.
I quickly became worried as I have my 3DS hacked to run emulators (namely for old gba games that I still own) and hacking my animal crossing town once in a while. Fortunately I was one of the few not affected by the initial ban and thusly have disabled wifi on my device as a precaution.
Some users have found temporary workarounds to get unbanned by changing their device friend seed. But until we're sure how Nintendo is determining which consoles to ban and prevent is (eg by filtering out which telemetry data the console reports), its advised against doing this as Nintendo could just detect and ban the newly changed seeds.
There are also posts on GBAtemp speculating the possible criteria for being banned here and here. The working theories are that Nintendo has been scanning through telemetry data the 3DS sends and then flagging any consoles with non-authorized apps (e.g. homebrew system tools, emulators, custom roms, etc).
It's also been speculated that this might be a reaction to the recent release of sighax/boot9strap, which gives users access to the 3ds early on in the boot process and allows for greater control over all elements of the hardware/software (including device encryption keys).
Nintendo's comment on the issue has been limited to citing a ban as consequence for terms of service violations.
While some are citing this as an anti-piracy measure, it stills fail in that regard as users are still fully able to install and play pirated games, though offline.