Systems left out of a sim don't even need to be Top Secret, any classification is enough to keep the information restricted. Confidential, Secret etc....
IFF, as a previous example, has restrictions on it, but the function is not classified. Mode 3 and C are available in the civilian sector and mode 1, 2 and 4 are generally military. Well...seeing that mode 4 was compromised, it won't be around for much longer.
Also, the export of information such as this is also restricted when dealing with certain countries. With the depth of this sim, I wouldn't be surprised in the US State Dept is involved.