As SpaceX has launched both NROL-76 and OTV-5, does anyone at SpaceX know the trajectory of the vehicle, or is the falcon upper stage under the direct control of the Air Force?
The way something like this typically works is that the customer, in this case the Air Force, calls the path classified, to some level. In the contract, the customer declares what parts are classified, and how such classified data should be handled. That will include the fact that any SpaceX employee that has access to the classified data must have the right security clearance, and the classified data must be kept on an isolated computer network. SpaceX then determines how best to meet the contract requirements, including any requirements to secure their launch permission. I believe for classified payloads they don't require FAA approval. SpaceX then reports on their findings, including simulations and such.
If the launch is very classified, they might even compartmentalize the data, such that those who know the trajectory might not be able to see the satellite they are launching, to keep things even more secure. It is very likely that those who actually loaded the satellite on to the payload require a security clearance.
Bottom line, some employees at SpaceX must have a clearance to know what the trajectory was, as they would be too involved not to know.