This sounds like just standard traffic analysis. Nothing to do with WhatsApp or any other messaging platform. It's been in use since at least WWII.

Who is talking to whom? How often? Under what circumstances? How do patterns of communication correlate with events? Who are the hubs of communication (ie leaders)?

The big difference between then and now is that instead of needing rooms full of people drawing graphs by hand, there is software to handle it. In turn, that means it's not really important to have initial suspects to get started, because the computers are quite happy to tease out interesting signals from total communications. That also increases the likelihood of false positives, but the kinds of people who do traffic analysis at this level aren't usually the kinds of people who worry about a little collateral damage.

It seems like a pretty tall order to construct a system of communication that is useful for coordinating activities, affordable to operate, and secure against traffic analysis. At best, you'll end up back in a situation where other intelligence will be required to identify a manageable pool of suspects.