The best practice would be for your program to invoke close() on the JanusGraph instance before shutting down the JVM. The close() method calls on closeInternal() and then removes the shutdown hook.

The shutdown hook is used because the JVM could terminate unexpectedly on its own or forcibly by the user, and the hook gives JanusGraph an opportunity to clean up. The shutdown hook calls on closeInternal() directly. Why not call close() instead? I imagine the call to removeHook() might throw/log an exception if the Runtime is already shutting down.