I asked Ahmad Zabarah (a Senior Designer) to share some more details about this change. The reason we removed the Commendations from Story Mode is that it is our goal to separate Story Mode Operations from Operation progression going forwards. In the previous setup, Story Mode was the best way to farm Black Hole Commendations, which wasn't our intent for the different difficultly modes. Going forward, Hard Mode and Nightmare mode will be the source of progression in Operations. We did, however, add Black Hole Commendations to the weekly Explosive Conflict mission, so you can also obtain the Commendations that way.
This doesn't explain why they were removed from Karaga's Nightmare Mode.