I own one of the affected repositories, and submitted the original link to HN the moment I got an email notification about it from Github [1]. It's a shame we didn't get the discussion going earlier.
IANAL, but what the hell does a security POC (and an unofficial API derived from it) have to do copyrights? On what grounds did a repo get chosen for takedown? Is it the "whatsapp" in the name? What about a simple "x.whatsapp.net" connection string in the code? Is that infringement?
Either way, shitty move by WhatsApp.