You cannot prosecute someone based on hearsay. In someways Whats App makes it easier because you could take the phone as evidence and see a record of all non-deleted correspondence complete with time stamp rather than trying to build a case based on two buddies grabbing a beer together.

Which is why a lot of these technologies are targeted. Not because encryption makes it harder for enforcement agencies since there's always been a plethora of ways to communicate in secret. But because gaining back doors to these applications makes it easier for them than it's ever been.

Sadly the point enforcement agencies always overlook is they're basically just fighting a game of "wack a mole". Encryption isn't something that's going to go away. Not even if you legislate against it. People know it exists and there are a thousand different ways to run software on your handset - even just via web sites directly thus bypassing all the controls for side-loading native apps. So all this posturing about the "evils" of WhatsApp is just a monumental waste of everyone's time.

IIRC unencrypted chatroom logs were used in the investigation against banks rigging FX https://en.m.wikipedia.org/wiki/Forex_scandal