Nagari doesn't filter anything, it just dumps thoughts into your head for your mind to translate. When Laporte pokes too deep and nearly drives herself insane asking about the Shivans, the Shivans cut her off. The Great Darkness is something beyond Shivan control, something that lurks in the collective unconscious of the universe, that is so fundamentally alien that it undermines a human's most basic grasp on reality. It's like telling a computer that two equals one; the logical incongruency is simply too great.
I wonder if even the godlike intellects of the Shivans and Vishnans can properly understand it, or if Universal Truth wasn't a near-miss for more than just Laporte.