OTP is considered the most secure method with a couple of caveats. There is a maximum length for each message. Each pad must generated in a way that does provide clues into it or others. The pads can never be reused.
Or the correct nickname for the NY Times: "The Grey Whore".
With burner phones, encryption is less critical because it is difficult to trace the phone to specific person. By regularly buying and ditching burner phones and careful sharing of the numbers it is very difficult to tie all the less ends together.
This smells of the DOJ surrendering. They lost key elements of public opinion and pretty much anyone who has fair understanding of cryptography. They also made it imperative the tech industry should push back in Congress which could really make their lives deservedly miserable.
There are several problems with academic publishing. First the publishers often charge the authors a fee to publish. Second the authors are required to surrender their copyright to the publisher. Third the subscriptions and charges per article are unaffordable for most individuals. Fourth, often the research is sponsored by a government agency thus the taxpayers. All are troubling but the last is most.
Also, the idea of publication and peer review is to get results and theories out to the wider academic community not to make a publishing house rich.
As far as breaking codes, natural languages have sound thus letter patterns in the language. If the encrypted text is long enough, the text will have essentially the same distribution as the language. Also, many encrypted messages, particularly government/military tend to have an internal structure much like a business letter. Both of these patterns give clues allowing code breaking. This was observed in the 1920's by William Friedman.
Also, the strength of cypher system is based on the underlying technology used to create it. Modern computer based systems are mathematically very strong for our current technology but they can be broken if one has enough computational power and enough time.
Back to San Bernardino, there is another rule about intelligence: it goes stale the older the information. Even if there is intelligence information on the phone, as it ages it will become much less useful overall.
Many very legitimate businesses will be essentially cash only dependent on the demographics and local area they serve. The problem is with bureaucrats who do not actually try to understand how many businesses work and why.