We should clear up the difference between a mute and a mute here.
Muting in a mixer does just that, mutes the audio so you can't hear it. However, muting in the sequencer has a different way of working. Here we're muting the actual "data", audio/MIDI. Try muting Thor in the sequencer and you'll see that Neptune stops responding.
If you trying doing the same thing you did with Neptune with ANY device (MClass Compressor etc. etc.) you'll see that they all receive signal. You just can't hear it.
In other words: this is by design.