Come to think of it, the Fadayyen not might be working on a superweapon at all. Too obvious of a plot point, and doesn't fit such a shadowy organization. (GTI Hades aside, but the GTI had a huge head start on the construction of their superweapon) In fact, some of the dialogue from the mission 'The Plunder' suggests that the UEF aren't stupid enough willing to put all their eggs into one basket like that.
All those resources are probably going towards something more subtle. Only thing I can think of that would require warships to continuously disappear and the resources of an entire logistics ship would be some sort of systemwide construction project somehow related to the Vishnans and/or Shivans. Such an undertaking would certainly require warships to fend off the inevitable raids, and the resources of a logistics ship.
This is going to tie in horribly with the Solis Lacus camps, isn't it?
It might be worth a playthrough with the mindset that things might be happening behind the scenes, and that the main character is an unreliable narrator. It's quite possible that Steele isn't the only grand chessmaster around.
Oh, and I am starting to think that the Fadayyen might be the Sol portion of what was once the GTI.