While that is always possible, I think its more plausible that they then simply buy out key companies rather than found a bunch of new companies in hope that one will succeed. The question then is, what is the likelihood that NSA is the secret owner and operator of Microsoft, Apple or Yahoo, which each would likely be the cost effective choice if one wanted access to all search queries done on the Internet.
Independent third-party auditing is useful. There is the occasional fund raising for auditing of software (Truecrypt comes in mind), but I don't recall hearing one about search engines.
