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.
Exactly why? Especially considering the absolutely ridiculous prices on the new implants for stupidly minimal upgrades. The justification behind those prices was that folks would now be able to obtain lots of BH comms in additional ways. I wouldn't really call this additional more than shifting it to higher difficulty content. And Group Finder content. Forcing people to run daily FPs, and weekly story mode original ops through the group finder really isn't the way.