Because you do the math on what kind of ripples you'd expect on something like two closely linked rotating black holes, then you find them and see if they match

Because you do the math on what kind of ripples you'd expect on something like two closely linked rotating black holes, then you find them and see if they match your measurement. I don't know what mechanism you propose for ripples in dark matter, but as they used a pulsars frequency as the sensor that would mean that dark matter was inbetween us and the pulsar and vibrating for some reason.