You used to be able to right click the mute button and change it to automated mute, then using the mouse write the automation like any other automatable parameter. Note that I'm on an older version of Sonar and can not confirm this behavior in Sonar X series but I'm pretty sure it works the same way.
As far as writing the automation from a control surface I'm pretty sure it's only available for the Cakewalk VS Series controllers. Like on my motormix, even though I can control mute via the control surface it will not write the automation.
Personally, I don't know why mute automation is a seperate control instead of one mute button that is automatable like any of the other automatable controls in Sonar.
This is a very old issue.