For scanning encrypted messages, they can be scanned on device before encryption, like Apple’s approach to CSAM.
[Edit] I evidently don't understand your remark. If some "encryption app" processes the plaintext before it is encrypted, isn't it processing plaintext between the keyboard and the encryption?
Directives have to be implemented in national legislation; it is customary for nations to ignore deadlines on implementing directives they don't like, and to finally implement them in a way that serves the interests of the party in power. So the national legislation is often full of loopholes, or provides zero mechanisms and funding for enforcement.
The EU does nothing to ensure that the implementing legislation actually implements its directives.
I welcome the GDPR (which is a regulation); I can't think of another occasion on which a piece of EU legislation I thought was good, has been handed down as a regulation.