The fact that “encryption” has lots of button-down business users, and isn’t just for cypherpunks and dark road drug salesmen certainly makes it harder to crack down on in broad terms; but it is often possible to add the backdoors or decrypt-on-demand mechanisms that team spook is looking for without necessarily upsetting the business cases.
Sometimes, that’s because the encryption already depends on fairly centralized 3rd parties who could be compelled reasonably silently(eg. Certificate Authorities unless certificate transparency is being done quite carefully indeed); in other cases it’s because ‘at rest’ encryption at one end or the other, or both, is weak or nonexistent; and the bulk of the effort has gone into securing traffic over the internet; in which case you just lean on whoever is most convenient for the at-rest records of what transpired over the encrypted link.
That’s why ‘end-to-end’(especially when ‘end’ is ‘phone with reasonably strong security design’) encryption displeases Team Fed greatly; while it is generally seen as neutral, or even encouraged, when more traditional designs(most email and IM that isn’t encrypted at the client, say) that allow for easy storage of messages by the provider add SSL/TLS to the link between the end user and the provider. Only criminals and opportunists benefit from having tons of cleartext flowing between you and your mailserver; and the feds don’t really care about how well that traffic is encrypted as long as they can just subpoena the server operator and get all the goods neatly packed for them there.
