Edit: I've gone through most of the relevant sections. Most of the ruling is reasonable, the section this article and the EFF are complaining about is less supported by precedent.
The actual legal argument says that hacking is common enough that people don't have a reasonable expectation of privacy, then there's this paragraph:
>Although this Court recently noted in dicta that the possibility of hacking "is not enough to defeat an individual's reasonable expectation of privacy" because it is illegal, see United States v. Darby, No. 2:16-cr-36, ECF No. 31 at 10-11 (E.D. Va. June 3, 2016), this Court stresses that child pornography often resembles an international crime. Similarly, much hacking occurs by foreign nations where the governments condone or participate in hacking. Child pornography is not just a national issue; it is an international issue, and at least a portion of the pornography in this case arrived from foreign sources through the World Wide Web
This seems to be the weakest part. It's saying that hacking can't be the basis for a lack of expectation of privacy, but that since some countries allow hacking, it's legal there, and if you're accessing stuff from other countries you no longer have the expectation of privacy.