Director's only storyboard VFX scenes because they basically have to. Many directors don't storyboard their live action because it's not an intuitive way to work for them. You also cannot possible forsee every single cut--it's inevitable that you would want extra takes and coverage when you get to post production for ideas or realities that you didn't anticipate in pre-production; even when you storyboard live action you still have all the dailies from the coverage. But it's too cost-prohibited to make visual effects the same way you film live-action. Kubrick was helped in that a lot of the visual effects were in camera, and thus needed no expensive optical composites et cetera and could simply be re-lit and re-filmed, and also by the fact that he had tons of money at his disposal. It's a way I am sure every director wished he could work. The way CG is going now, this is actually starting to become a bit of reality--for instance the virtual camera device that filmmakers like James Cameron and Peter Jackson are using.