As we reported yesterday Nintendo is currently doing a pretty big and widespread Banwave against 3DS Users with CFW. Over the Night a bit more Information has been gathered as to why the bans could happen. There is still a lot of speculations regarding the cause of the Bans but it’s pretty hard to find one. 
People from Firmware ranging from 11.2 to 11.4 have been banned so far, People with different Unsigned Code Execution Methods like HomeMenuHax, Arm9LoaderHax, Boot9Hax have been hit, People with different CFWs and CFW Versions as well as People using Freeshop and People not using Freeshop.
https://twitter.com/ChrisHighwnd/status/867826677925244928
As you can see there are many aspects so it’s not that easy to find a common cause yet as to why all the 3DS Consoles are getting banned. The currently best List of reasons and how you are maybe at the safest spot to not get banned has been posted by Astronautlevel and Syrocil on GBAtemp:
Joke:
“You will not be banned if you:
– run homebrew from within another app (browser exploit, or cubic ninja, for instance)
– install b9s by running homebrew within another app, or outside of the 3DS environment (from arm9/boot9, hard mod or DSi mode, for instance)
– play cartridge games
– play purchased eShop games
– play “legit titles” which are preinstalled on your 3DS
You may be banned, if you:
– install homebrew titles, or install titles/tickets which you own
– run apps from the home menu that you do not own
– run homebrew applications from the home menu
– manipulate data being sent to the friends/presence servers
– cheat online
– play games before their release
– pirate games or DLC
– mess with ticket data
– follow The Guide at http://3ds.guide/ and perform the steps which install CIAs, and applications to your home menu.
We do not presently know how Nintendo determines which consoles to ban. They can look at any data sent from your 3DS, to or through their servers. This includes, but is not limited to:
– Friends list data, presence information, Favorite Title information, Now Playing information, game/battle join information. This includes your currently running title.
– Matchmaking data for all games. This includes your current playing game, ranking and player information, DLC owned, and so forth.
– SpotPass (BOSS) service subscription data. This includes all titles you have installed, which have SpotPass enabled.
– StreetPass service beacon and user data. This includes all titles you have installed, which have StreetPass enabled.
– eShop, DLC/eShop Applet, and Theme Shop, when launched, may send a list of installed titles and themes to Nintendo.
– When the system checks for an update, it retrieves a list of title versions. This request should not have user-sensitive data.
For your safety, we recommend that you disable wireless services until further notice”
In another post he also mentions that the Use of Freeshop has no connection to the bans:
As you can see there are currently many ways suspected to get you banned and only very few said to not get you banned so it would be best to follow Astronautlevel’s and Syrocil’s advice and turn off your 3DS network functionality if you really want to stay safe. You may still be banned but the risk is a lot less high if you don’t connect to the internet at all on your 3DS anymore as long as this Banwave still continues.
Source: GBATemp