People may not exactly know who dark matter is but he has henchmen, thus people do know about him to an extent. 

Another thing that makes the complex so secret is that data wise, not a single member they have exists, no finger prints, birth certificates, anything about their identity belongs to the complex because that is where they are born and raised. The titans and even dark matter could look up Jack Maverous but there isn't a single thing they would find. Maybe another guy with the same name because that is quite common in society but that would throw them off completely.

There is a reason why I said the complex has their own intentions and their own way of doing things. They have no connections to any organization. That can be bad in terms of resources if not handled properly, but if you don't work with anyone, it makes it that much harder to find out who you are because there isn't a single person who has ever heard of you. Imagine what things you could pull off if no one ever knew you existed and won't ever know. You can't interrogate people because to find out info because no one knows of them. You can't report something that doesn't exist.