Different groups working on different projects, lack of communication and global company vision or even internal competition leads to wasting money producing the same thing multiple times.

Basically the "Not Invented Here" syndrome, at the company level.

Although fun to say "the left hand doesn't know what the right hand is doing", I think it's unlikely that the designer for Messenger didn't know that Facebook had emojis. In fact, the Facebook and WhatsApp scissors look similar enough in style that I wouldn't be surprised if they were drawn by the same person.

I think the real answer is that they are 3 products with 3 different target users, and Facebook really wants to keep them separated in the minds of users (to keep bad karma from one brand tainting another). So, "brand differentiation".

It's because they learned from how other dotcoms failed to capitalize on acquisitions by plastering their brand all over them and making them an appendix of the mothership, that would then usually wither and die.

The most lucrative decision that Facebook ever made was not messing with Instagram, but keeping it as its own separate brand. And with that goes that it should have its own visual identity. Then they just applied the same thinking on several of their other properties.