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.
Thanks for the info.
Although...this was not a good idea IMO. This is making your old content less desirable to run, and it doesn't make any sense that SM EV and KP will offer a few BH comms (through the LFG tool) but SM EC will not.