From Apple "The M9 motion coprocessor is integrated directly into the A9 chip so you can do more, for longer periods of time, with great performance and battery life. The M9 connects to the accelerometer, compass, gyroscope, and barometer for a wide range of fitness tracking capabilities. With iPhone 6s, you can now measure your running or walking pace in addition to your steps, distance, and elevation changes. The integrated M9 works so efficiently and intelligently that Siri is always on and waiting for your voice commands. You can easily activate Siri by saying “Hey Siri” whenever your iPhone 6s is nearby."
Reading that, it does not connect to the Microphone, it offsets power requirements for the main CPU.
Or, maybe it motion detects when you are about to speak. But that then would mean Siri ignores you if the phone is sat on a table.