Does the H9 detect the mono (or stereo) input based on if a plug is inserted, or if there is an input signal in the channel?

Yes, the H9 detects the mono/stereo inputs based on if a plug is inserted.

If you want to run 3 H9's stereo effects, you may just put the third H9 after the output of your ES-8. You may use MIDI to control its on/off and switch presets.