I've seen first hand what creative people have been able to do with their 3DS with just a few modifications. The system is a powerful little sucker if you take the training wheels off, but it can also do some really illegal stuff as well. Nintendo knows this, which is why it puts restrictions on it in the first place. But now, if you're one of the many using illegal software or other modifications, your account could be banned!
Nintendo has quietly started a new initiative to ban users who have devices with unapproved mods on them, which are hardware specific and limited solely to the modded 3DS and not a NNID, so your game library is intact. Word has been going out on social media that modded devices that have not taken part in any kind of piracy are being included in the ban, which basically disconnects you from being about to use wifi, even though the eShop still works for many.
Those crying foul at Nintendo going after the modding community may have just cause to say they are, however, Nintendo has very little choice in the matter. Since you can't specifically see every single piece of software a player may be holding on their system, it's hard to remove people with pinpoint accuracy. So instead, Nintendo have whipped out the ban hammer and is taking it to everyone they can in hopes of squashing illegal activity altogether.
There are currently discussions happening on several sub-Reddits the homebrewer community is looking into if the bans are even legal with the iPhone soft-mods serving as a legal precedent as not breaking warranty or a TOS. There's also the discussion of just how Nintendo discovered the mods to begin with and are suspecting the SpotPass or data sharing options as the culprits. Regardless of the current situation, it doesn't seem as if Nintendo will be letting up anytime soon, and the homebrewers are looking to fight it anyway the can.