I'd say the big problem in visualizing big systems is that you can't usefully do it in one graph. For instance I worked on a system that had 2000+ database tables if you were going to make a diagram of that which shows everything it is going to take up a long wall. (This can be useful, but it is a big commitment)
A useful tool is going to let you make meaningful diagrams that show the subset of entities that are part of a story. I went to an art show of Mark Lombardi's works
https://en.wikipedia.org/wiki/Mark_Lombardi
who (before he was murdered) drew elaborate diagrams of conspiracies. One thing they showed was drafts that he made in the progress of creating his visualizations and he would sometimes make 40 or more of them. He would start out with a "hairball" that was disorganized and gradually figure out how to lay the diagram out in a way that made the meaning obvious.