So pretty much the bottom line is, if anyone has been using custom apps and/or titles not installed through Nintendo eShop while online in the past, guess what? You're screwed! And it is only a matter of time before your console's unique hexadecimal ID in the LocalFriendCodeSeedB is banned from Nintendo's online gaming server. This will mean, your console can't access the Friend List or play any online functions in games.
If you have been online while using custom apps and/or titles not installed through Nintendo eShop and haven't been banned yet, that's because Nintendo hasn't caught up to you yet. They're still going through each unique hexadecimal ID's Activity Log on their server, and by Activity Log, I mean the Activity Log on their server, not the 3DS console's activity log. And it will be only a matter of time before you're banned too.