I worked with a core group of people that were responsible for IT in the Executive Office of the President under Bush II, but left in the wake of the missing email scandal. They were some of the most extremely bureaucratic IT people I've ever met. They all were incredibly hard workers, but fundamentally in the box thinkers. The way they implemented Microsoft security could be classified as insane. Locking down stuff to the point where it just wouldn't work any more. Forget being an admin as a developer, you had to ask for temporary permission to launch a service on your server. They had incredibly cozy relationships with the Microsoft sales team, and many ended up working for Microsoft after they left.
Do you have the impression that the missing email scandal was a technical lapse or politically motivated? I know it's widely assumed to have been the latter, but it's often easy to overestimate these things.
I don't have any insider knowledge of the Bush admin's controversy, but I have seen and heard of cases in the corporate world where similarly draconian admin policies that forced users to jump through hoops in the name of security often had the effect of driving users to adopt easier and less restrictive external services instead. I suppose it's not impossible that something similar happened here, but to be honest senior admin officials really should have known better even if that was the case.
It could easily have been either, but I think they knew they had a weak archive strategy, they just didn't do anything about it because it wasn't a priority to save those emails.