Alternate theory:
We don't know how long it took the GTI to build Hades. Silent Threat was... a couple months after the end of FS1, right? The GTI probably had been building the Hades for a very long time before FS1 ended. They could have grafted the Shivan tech on later, after meeting the Shivans. They may even have been researching the Shivans before the GTA at large discovered them. After all, there were rumors of "phantom ships" attacking Riviera Station long before the Shivans made themselves known to the Alliance at large. What did Command do? Probably under orders from GTI, they tried to quash the rumors.
I think the GTI Rebellion was in the works for a long time before the Great War (that is, the war against the Shivans, I'm not talking about the T-V War) even began. The Great War probably even slowed it down a bit; common enemies and all that. The Hades was always gonna be their main weapon, developed in secret, and the Shivan tech it was using was simply an added bonus.
The Shivan research was all locked up by Command, likely in the hopes of preventing another GTI Rebellion. Therefore, construction of the Hades as it was would be impossible unless the Shivan research was unlocked again.
Take a look at this, part of the Tech Room description of the Hades:
After the defeat of the GTI and the destruction of the Hades, the GTA classified the details of this research at level Omega. There are rumors that the Alliance has attempted to reconstruct the Hades to learn more about the GTI's activities. These reports have yet to be confirmed by government sources.
Don't know about you, but that makes me think that the Hades might have reappeared in FS3, had it ever been made.
[/speculation]