The difference is whether the entire organisation would have to know or not. "Actually, our HDD factory is operating" is both a thing that lots of employees would necessarily know (unlike CIA assignments in Canada), and also those employees would not be as trusted as high level intelligence agency operators. Particularly for low level employees, like contracted cleaners or whatever "Don't tell anyone the factory is operating" seems like it would be a great way to get the information out there that it actually is.
You tell the employees that they are working for a HDD factory. A small number of people at the top of the company are in on it and keep sales limited to one or a small number of clients, all of whom are the clandestine buyer.
That would be similar to the way in which the fake Swiss cryptographic machine manufacturer was run. Their only leak risks were from employees who realized that their cryptosystem was easily broken. An HDD manufacturer would not have that problem because all of its work would be perfectly legitimate.
