This is an easy one: (via Chet) When a government has been committing human rights abuses and hasn't kept any files, it's because the crimes they committed were so bad, they hoped they'd never come to light. Look at the history of torture throughout the 20th century, and 2 things are incredibly common. Either a) the regime never kept files, or b) if they did, they were destroyed as soon as the tide turned. The Bushies apparently took the safer route.
And yes, keeping no organized comprehensive files, given the labyrinthine nature of the US government, is the same damn thing.