Hey Joost,
I just fixed this issue in another plugin that wasn't registering a hook with the wp cron action, and I think the issue in WP SEO not firing the wpseo_ping_search_engines cron job will be fixed in the same way.
We simply need to hook it in I think.
You'll just need to add something like this:
add_action( 'wpseo_ping_search_engines', 'wpseo_ping_search_engines' );
That should register the hook and enable the cron job to fire as right now I don't think it is when a new blog post is posted.
Let me know what you think.