Over the ages there have been countless secret societies, some of which exist to this day in varying degrees. Of those you mentioned, all are or have been real at some point in time and are somewhat related to the roles portrayed in Brown's books. That's where fiction kicks in and makes use of specualtion and literary license to raise real questions among us.
As for conspiracies, until something is proven, they mostly exist in our imaginations. However, there must be some purpose to keeping closely guarded secrets. We can only speculate whether such secrets are to guard the security of something really important, shameful, harmful, or just to create an elite among members. In any event, I tend to be suspicious of any group that feels they need to hide something.