The short answer is that as the many stories by the IntlSpyMuseum in Washington demonstrate, organizational secrets are a very unreliable tool even, if all, who are authorized to get access to them, are screened properly, because in addition to spies the authorized personnel can be just plain stupid, careless or their political views can change over time. The best spies get caught by being revealed by incompetent or just plain careless co-workers or defectors, which means that actual secrets should never be shared with anyone within the spy organization, despite the compartmentalization efforts. Compartmentalization also comes with the cost of suboptimal use of team mental capabilities and poor oversight of the situation.
On the other hand, it is known that the extremely hierarchical Chinese Communist party is accused of introducing secrecy based inefficiencies. That statement probably holds to all dictatorships and the Russian political elite. It's the secrecy that cost the Soviet Union the Cold War with the United States, because the research and development efforts that led to the superior weapons of the Soviet Union, did not get transferred to the service of the Soviet Economy, whilst in the United States the the military research and development results found their way to commercial products, giving the United States an economic edge. Of course, the Soviet Union was based on oppression, which set its limits on the technology that the Kremlin dared to let the general public use. For example, computers were seen as a threat to the Soviet communist regime and typewriters were regulated despite the fact that equipment and materials for developing paper-photographs was widely available and totally unregulated. You can just imagine, how efficient the planned economy might have been, if it had been operated by using computer networks and data analysis, various computerized optimization techniques and a giant communist Alibaba. (I guess that internet banking would have been ruled out, because the Russians are too corrupt due to their hierarchy-loving culture and the internet banking would have limited the corruption too much.)
If the number of people, who know a common secret, is "big enough", then it is possible to extract it by torture, the way the French army did during the Algerian war. The scheme is that if the torture victims speak the truth only 3% of the time and rubbish during the rest of the time, then it is possible to look for common data points between the statements/out-cries of the whole set of torture victims. To minimize the torturer induced common data points, the amount of torturers should match with the number of torture victims and no torturer should receive any common instructions for the "job" and the torturers should not originate from the same army unit/intelligence agency branch. (The discussion about, whether torture is acceptable, should not be based on whether torture works, it does work mathematically. The discussion should be based on the essence of ourselves, whether the way we want to define ourselves, allows torture to be used.)
The summary is that the organizational secrets as a tool best serve hierarchical, oppressing, organizations, where even the details of corruption is a set of data that needs to be kept a secret. Non-hierarchical organizations/teams should just declare that there are no organizational secrets AT ALL and be extremely careful, if not paranoid, about keeping personal secrets only to themselves, id est the privacy issue is essential. The tax based supermafia gangs, generally called as governments, will never run out of money, but the most critical economic resource is always the required resource that will run out first, which means that economically the tax based supermafia gangs can still all go bankrupt, despite never running out of money. (Have You ever thought of spending suitcases full of Euros or Dollars on the moon, while You are the only person sitting there and there are no cargo shipments available, except the rockets that can not transport You, but can transport Your money bills away from You?)
Improvement on 2015_12_23:
The IntlSpyMuseum has a presentation with a title "Why Intelligence Fails". My 2015_12_23 summary of it is that the cultural background of the analysts determines the questions that they try to find answers for and in the case of major failures, where the intelligence agency staff itself is not able to anticipate the events, the set of questions is incomplete.