Describing a project as "working with WhatsApp" would probably not be an actionable trademark infringement. Code that works with the WhatsApp API is almost certainly not "infringing", unless there's some "encryption" going on.
Unfortunately the DMCA takedown rules are such that Internet providers such as Github have basically no direct recourse and refusing to comply is not an option. Additionally, complainants don't have to prove much of anything to issue a takedown notice to a service provider. This is a seriously broken part of copyright law, IMO.