What shocks me more than anything: we're dealing with PAPER apparently! Why aren't these documents digitized? .PDF format? Why are there no backups at a secure facility in Colorado?
It appears that if Sandy Berger "got to" every copy at the National Archive, then (perhaps) some of this information could be lost forever! HELLLLLOOOOOO! It's the 21st Century! It just shouldn't be possible.
You are making an assumption that may or may not be true as to whether all documents are digitized and stored elsewhere.
One problem with digitized docs and microfiche - they are more easily accessed and/or concealed by unauthorized people. In terms of digitization, they are also more easily erased.
Physical security of the computer itself is moot if the computer is connected to a network.
Electronic copies of paper originals (i.e.: the notes hand-written in the margins) would be an excellent idea, but not without security risk.