Is there any down side to robbing black markets?

Some of the black market dealers will ask you to do things for you or have unique dialog. If you rob them, and the method by which you rob them spooks them into running away, you will potentially lose access to those quests or dialog if you haven't yet experienced it.

(Particularly since, I've noticed so far, many civilians stay in their "scared and running away" state basically forever and never return to their original behavior.)

It's also possible that opening the shutters & stealing from their shelves without scaring them off prevents them from selling you any more of whatever you stole, but I have not been able to test this yet.

On additional downside I've noticed: You steal all the gear in the case, but lose access to purchasing active blueprints, including new ones you might find later in the mission.

In my case I found a new blueprint, and had no way to purchase it. I would assume they would be purchasable at the next black market instead, but I haven't played that far yet.