[denizener]

Any of the python network science libraries can handle a 1000 node directed graph no problem.

Networkx visualizations are ugly out of the box but you can make the network look however you want. The best out of the box visualizations I think are a matter of taste and use case. Same with the layouts.

In a more abstract sense, I think it is hard to not have a 1000 node network visualization not be a useless hairball unless the network is quite sparse.

If you mean with do-calculus though I really have no idea.