I haven’t been able (and haven’t really tried) to discern a pattern either, but I don’t think it has to do with WhatsApp web or WhatsApp being open when I locked the phone. If that was the case, I wouldn’t get an audio notification either, but I get one without fail. On my old phone (Samsung S7) the LED would flash every time I got an audio notification.
What’s more, I have some WhatsApp groups set to ONLY notify me using the LED. This used to work fine on the S7, but hasn’t even worked once on the FP.
To be clear, this is as far from being a deal breaker as can be. On the contrary, it’s only because my FP (which I only received a few days ago) works so surprisingly well in almost every regard that I notice such little things 