I'm not doubting that it's a single threaded AI, Mussles.
They would have to completely rip apart the engine to multi-thread the AI, something they probably did not want to undertake for this expansion.
If not coded to perform near perfectly, which would require an incredible amount of testing given the complexity of the game, it would end up a disaster. I do not know what the sales figures are like for SoaSE, but it's quite possible that the cost to rewrite and test the engine in such a manner would be so high that they would never recoup the investment.
That would be bad for IronClad and Stardock ... really bad.
I know about the slowdown when there are hundreds of ships in SP, but MP (which I have never played) has got to exacerbate that problem with the game requiring the constant sending and receiving updated positional and status information for/from all of the players' ships and planets.
When considering everything that is tracked in game, I have to give them credit for it working as well as it does.
Anyway, I finally had a little time to re-familiarize myself with the game so I'm off to have a great time getting my ass handed to me.
Perhaps some day it will sink in that retreating and regrouping is not dishonorable and that "Death Before Dishonor" isn't always the best tactic.