I'm new with Hauptwerk but I'm having this same issue. I drive the Launchpads via USB from an OWC Thunderbolt 3 dock. I've been using the following work-around. I can just shut down Hauptwerk, pull the Thunderbolt cable out of my laptop, and immediately plug it back in and restart Hauptwerk. This recycles the Launchpads, making all the unused switches 'dark' again.
It certainly would be nice if the unused switches would turn off when a new organ loads, but I can get around it quite easily. Perhaps you could do something like this too. Even without doing this, the lighted but unused switches are just a little distracting - they don't cause any issues.