Apparently, Nintendo's notice reads:

The freeShop application provided at infringes Nintendo's copyrights, because the application circumvents Nintendo's technological protection measures in violation of the Digital Millennium Copyright Act. Nintendo encrypts the game files available from its eShop servers to prevent users from accessing those files without paying for them. Nintendo believes the freeShop application circumvents Nintendo's protection measures by decrypting the game files accessible from its eShop servers, allowing freeShop users to access and play Nintendo's eShop games for free.

The freeShop application also contains unauthorized copies of the Nintendo 3DS Logo Data file, covered by U.S. Copyright Reg. No. PA0001781880, which further infringes Nintendo's rights.
The Cruel - the creator of the Freeshop Github page - has reacted angrily to the news:

If anyone wants to know whether I'm going to counter it, I'm not yet sure. That could permit them to file lawsuit against me...to claim [Freeshop]circumvents any protections is laughable, though I'm unsure if it's legally sound (law is often laughable itself). It only circumvents protections if people utilize title keys they did not purchase or obtain legally. If people illegally obtain the password/PINs of a person's bank account, you can't criticize the banking website for facilitating theft.

QUELLE und TEXT: http://www.nintendolife.com/news/2016/1...