I wouldn't read too much into this. As part of their purchase agreement WhatsApp likely needed to say that they had been diligent in maintaining and defending their copyrights and trademark. That's pretty standard in a financing, so I'd imagine it's a standard part of M&A deals. It probably turned up during due diligence that they had some "cleanup" to take care of in order to not be lying when they made that representation.
It's pretty disgusting to dismiss this level of abuse of the DMCA (these aren't even legitimate copyright issues!) and legal bullying under the guise of standard operating procedure. It's over-the-top wrong.
