For some reason, the government did not appear to make the argument invited by the Supreme Court by its rulings in the FedEx and dog-sniff cases. The government could have argued that -- if the EnCase scan for a particular MD5 hash matches -- that the search is constitutionally permissible without a warrant because it revealed nothing except the existence of contraband. And, because there is no reasonable expectation of privacy in contraband, the government might argue, a search which only reveals the existence of contraband invades no legitimate privacy right.
In the Crist case, however, the court never addressed that critical issue, because it never had to. The government merely argued that an automated search was no search at all.
This unanswered question -- whether a scan of hash values looking for contraband is a permissible search -- is really the rub.
If the government may conduct warrantless searches as long as they only reveal the presence of contraband, then they could lawfully put automated sniffers on any computer, searching for the presence of files for which the MD5 hash matched that of contraband. While the software categorizing the files might be considered to be conducting a search -- and I think it is -- the contents of this search are not revealed unless the program believes it is contraband.
... ... How did I not see this earlier? Pretty sure this is the same guy writing about how data stored "in the cloud" can be legally searched without a warrant because you have involved a 3rd party who can consent to the search.
And don't think about kiddie porn. Think about the MPAA.