The case, led by a special agent in the Commerce Department's Bureau of Industry and Security, focused on claims that some Meta employees and contractors could access...
A 10-month Commerce Department probe concluded Meta could view all WhatsApp messages in unencrypted form
That, and if WhatsApp has the keys, then no amount of encryption is going to help.
If I remember, the allegation was that they did keep all the keys and many employees could request them to decrypt specific sessions.