I suppose it's true decrypting the files is not so much "circumventing" the encryption as it is... decrypting it, but I think for the purpose of the DMCA it's the process of "circumventing" Nintendo's attempt to keep unauthorized people from playing these games that it's referencing. Encrypting those files is a part of their DRM scheme, so they say undoing it without their authorization violates the law. That's my understanding of their claim, anyway, and part of the basis for their previous DMCA takedown notices to github. I don't think this specific claim has ever been tested in court.