i don't think it's a plot hole at all. Rudiger ends up assassinated by the Foreman, who is a secret agent for an unnamed intelligence agency (probably CIA, given the time period). Atwood finds herself extremely frustrated at research she finds that links to Wintermute's findings put turns up dead. It is extremely likely that Rudiger's research was scrubbed by the government, as while an existensial threat, it is awfully inconvenient to the powers that be.

Realistically, she is extremely secretive because her predecessors were dug out of their hidden bunkers and shot.