Hey, first post here, long time lurker. This thread got me deeply interested. The storyline of FreeSpace and the enigmatic Shivans is one of the things I think that has kept my interest in this game ever since I played FS1.
Anyways, I think it's highly unlikely the pilot in the opening cutscene was attacking a Shivan warship. The pilot makes the flat statement that "we were in a skirmish with a Vasudan patrol, and they just came out of nowhere." Considering this pilot is scared ****less I find it hard to believe this is all acting.
Also, I don't agree with the theory that bombers would have only been sortied if there was legit need for heavy bombers (in this case, attacking the Lucifer). The Apollo bomber variant would not have been a heavy bomber by any stretch of the mind, and most certainly after 14 years of war would not be the heaviest attack craft in the GTA arsenal. More likely it was a support wing deployed with standard fighter wings to provide heavier firepower should it be needed if the patrol encountered something like an Aten cruiser.
I do however agree that the GTI knew about the Shivans, or at least had some idea, prior to FS1. I find the best evidence of this is during one of the command briefings where Admiral Wolf mentions "There is to be no more talk of phantom ships." It was made pretty obvious that there were no survivors from Ross 128 ("The investigation of the Ross 128 attack has turned up nothing"), or, at the very least, nothing that wasn't classified by the GTI. So where did this talk of phantom ships originate I wonder?
Anyways, that's my $0.02 on the current angle of this discussion.