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.
What an awful change. We are still working on this operation since we are a bit behind and the coms were a nice motivation for everyone as it meant all players got something at least for their runs or partial runs.