According to company reports from September 2017, WhatsApp had 1.5 billion monthly active users and Messenger had 1.3 billion. So, why doesn’t Facebook integrate WhatsApp and shut down Messenger? The answer might be that they would likely upset a lot of users - over a billion, if one or the other were to go away. Facebook already upset a lot of WhatsApp users by sharing their data after they had pledged not to do so when they purchased WhatsApp.
Also Facebook makes money by allowing advertising on Messenger whereas WhatsApp users have not traditionally had to see ads appearing every time they use WhatsApp. Needless to say there are many integration issues that need to be worked out.