If you just “Play” the song it is normal that renoise does not send MIDI data to the midi device if you shutdown a whole track. If you would stop a sub-channel i would not expect it to behave otherwise.
I have actually not tried what happens if i record notes in a main track where sub-channels are muted.
just make a track with, let’s say, 4 note collumns
set the second one “off”
go stand with the cursor on the first collumn.
now just play some notes while controlling a midi device,
you will notice what I mean, I hope.