I do have an update on this issue. This change was intentional, and we'll be adding it to the patch notes. Bosses in Story Mode Operations no longer drop Black Hole Commendations in Game Update 1.4. Thanks to everyone who brought this up, and we apologize for the confusion over it.
I don't understand this Bioware policy of making it harder to gear up. All this does is encourage people not to run Story Mode. Wasn't it said earlier that by adding in the new Operation "Terror from Beyond" that getting more blackhole commendations easier and faster would be possible? That's not true if Story mode no longer gives any blackhole commendations.
I just don't get it. I respectfully request you change this back.