The outer stack is pretty big as it is, so it seems like odds of them both coming out are slim. Even if they did, I don't see why that might be terrible.
In my games I just leave the tiles with all the other III-hexes. They get into play randomly. Usually I have no black holes in the game and several times I have had 1. I have never played a game with 2 black holes, but I guess with more player count it is more likely than with less. I think it has worked quite well.
I usually play with 4 people.
I also own Rise of the Ancient and Shadow of the Rift which means I have quite a lot of III-tiles.