Yes, this is an affirmation that encrypted data is a sign of guilt until law enforcement determines that it is not, that is, when the data has been decrypted and evaluated. It is not a far step to also claim that use of encryption devices and programs, passwords and biometrics, would also be signs of guilt of a suspect until proof of innocence is provided that satisfies authorities.
I do not know what legal authority there is for holding onto encrypted data that cannot be shown by law enforcement to be any of the five things listed in the FBI affidavit. Mere encryption is not a crime, is it? This development is similar to anti-circumvention provisions of the DMCA in that innocent circumvention is by definition not acceptable to copyrighted content authorities. This demonization of encryption and circumvention until they have been exorcised by official and commercial authorities is similar to the provision which allows the NSA to collect and retain encrypted communications forever, even that of US Persons, no matter what purpose unerlies encryption use, though collection of non-encrypted communications of US Persons is proscribed. This open-endedness of stigmatizing crypto is diabolically wondrous, for it places the burden of innocence on anyone who attempts to exclude oversight of authorities of personal information. And reminds of the terrible deeds of the medieval church -- spying, ratting and testifying on neighbors, inquisition, torture, execution of those who defied supreme authority, not by physical actions but by words of dissent, words plainly understood in comparison to the arcane Latin of the secret keepers of privilege, luxury and perquisites. Try to imagine that all national security information was open from birth and only became secret by common judgment of its value, rather the reverse policy now in effect by which a small cadre of secrecy priests maintain a cloaked procedure for deciding what the citizenry can know. And that anyone who defies this culture of secrecy shall be considered guilty before trial and public judgment.
