I don't work on GraphDB, but basically the situation is this: 1) yes, it is not a great use case for MySQL, but that's how it started, partly because Twitter needed join on its graphs; 2) legacy systems die hard, especially at scale- Twitter is working on a better solution, but for now Flock is still what's running in production.

Thanks for explaining. I had a similar situation -- storing a graph db in postgres. The performance sucked, but we didn't have much of a choice.