1. A derelict, and probably just that. Probably abandoned and nobody bothered to tell the authorities about it.
2. The corvette Ithaca was destroyed by the MYSTARY Faustus (which, if you check the mission in FRED, is actually the MTSC Impresari).
3. If the Nyarlathotep was the Lucifer that destroyed the Ancients, it probably served no use after it accomplished its mission and was sent into subspace to be useless for all eternity (since leaving it lying around would be very dangerous if it fell into the wrong, non-Shivan hands).
Who can really say how the Destroyers think and why they do the things that they do?
5. The Shivan ships were floating around, unused, in the far corners of Phi Eridani and perhaps the other Tau Sigma systems. The Nyarlathotep's distress call probably reactivated them and brought them back into active service.
The other questions will presumably be answered in Blackwater Operations.
My own interpretation is that Morgan Technologies was nothing more than a front for a rogue element of GTVI who wanted to secede and create their own Tau Sigma empire. The loop was not a deviation from the plot, but a glimpse at the treachery soon to be exposed. Presumably the many shenanigans the rogue Intelligence faction is pulling during the loop are attempts to assist the Auriga - ambushing the beam inhibitor convoy and disappearing the survivors, stopping the GTVA AWACs ships from locating the Auriga... the Deus was probably really from GTVI High Command, though, and just cleaning up the scene of a delicate, sensitive situation.
That's my theory, though. I didn't make this or nothing, see, so I'm talking out of my goosepipe here.