That question is prompted by this post questioning the number of different offices Obama has created in his executive office (EO).
I remember reading something once about the evolution of offices. I think the writer started with Britain, which has a long history, and traced the evolution of the cabinet and various positions. (For example, Lord Privy Seal used to be the monarch's "body" man, carrying the official seal of office. Then it evolved to a more bureaucratic position and lost its eminence. )
Part of the argument was to the effect an effective cabinet needed to be small. A "Decider" will abide only a handful of close advisers. George Washington started with a cabinet of four people, secretaries of State, War, Treasury and Attorney General. (Maybe 5--Postmaster general.) And Hamilton and Jefferson were his early advisers. But, gradually, the cabinet offices became more bureaucratic and, by the time of Andrew Jackson we had the "kitchen cabinet" developing--a handful of people, some with official positions and some without, who worked with Jackson.
That trend has continued--Presidents aren't about to risk their reelection and legacy to the abilities of their cabinet officers, so they create more assistants and offices in their own office. (Clinton campaigned against the trend, promising to cut the EO by 25 percent, a rash promise that contributed to his early problems.
Back to the question--as a bureaucrat I'd define a "silo" as an organization which hires, trains, and promotes its own people. The Marines are a silo, NRCS is a silo, etc. People imbibe the culture and drink the Kool-aid when their career is spent within an organization. That isn't likely the case with the EO people, even though the proliferation of offices is likely to lead to other bureaucratic problems.