Why would it be expected that do-not-disclose agreements cover all employees or owners? Most top secret information is handled on a need-to-know basis; it is only given to people who are deemed to need to know it. Even within IBM (or any other large company that was involved in PRISM or other NSA programs), most people in the company wouldn't know about it. In general, there are only a few people within the company, who have a secret or top secret clearance, who get to know about what's going on.

Furthermore, owners don't know everything about a company either; shareholders in a public company have no greater insight into the company than the general public.