This is perhaps true, yet to the same extent that it would be true of any other secret weapon's deployment.
For example, let us consider the development and deployment of Stuxnet to be analogous to a miniature Manhattan Project. What proportion of the physicists and engineers in the Manhattan Project do you think were aware that they were building a large bomb? I would guess as much as 20% of the personnel directly involved with development knew what the project was. This includes the "integrators" - project managers and people in similar roles that need to know how different pieces fit together. I imagine the same is true of Stuxnet.
