I've generated diagrams from various sources of data in AWS (security groups, EC2 instances w/ their attached security groups, edges between, etc) and never run into this issue. I'm talking thousands to tens of thousands of nodes and tens of thousands of edges.

The utility of these diagrams was limited, given how dense they were. I'm curious what use case graphviz chokes on that would generate legible graphs..

edit: this reminds me that it would be useful for the AWS APIs to return a "modification epoch" number inside API responses, so that while you're enumerating/describing thousands upon thousands of resources, you could at least keep track of whether there have been any modifications between your first and your last Describe* call.