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.
Mitigating the security risks is not easy, and not cheap -- but at Sandy Berger's level, it should be routine. The idea that one guy can stuff a few copies of a memo down his pants and "poof!" all knowledge of such a memo is forever gone is just shocking. I do not know what procedures are followed at the National Archives, and perhaps they are smart enough so that nothing was actually "lost" -- but the news coverage seems to indicate that Berger did some irrepairable damage to the Archives. All I'm saying: relying on paper is barbaric.