In my most recent game, the Drengin were one of the last races I conquered. On entering their territory, I noticed a stack of about a dozen fleets of 9 super-dominator corvettes each. One of my huge ships chewed through them in about a week and a half, and it was good.
Then, near the Drengin homeworld, I noticed 3 *more* stacks of SD corvettes, each with about a dozen fleets of 9 corvettes each. "Oh, what a PITA" I thought. These ships are totally irrelevent, but at least it won't take long to kill them all.
Then I made a terrible, terrible mistake. I conquered the Drengin home system, thus defeating the Drengin empire. Of course, all those zillion corvettes were now pirates, organized into fleets of size 1. Talk about a pointless headache. Just looking at that section of space bogged down my machine, and it would take real-time hour to kill all of those pointless ships one at a time.
The point: Is there any chance of changing Super Dominator so it's keyed somehow to your current tech level? Say you have 13 hardcoded designs for an SD corvette: one basic design, and 4 designs for each of the different weapon types. The designs are organized in increasing tech level. So you have SD corvettes that use lasers, phasors, etc.
When the SD ability activates, you get a batch of ships of your highest accessible design. The key point is that the batch is scaled so that it has the same military rating as whatever you would get with the current SD corvette design. That is, you get more effective ships at a higher tech level, but many fewer of them.
I think this would keep the SD ability relevant and less annoying in the late game.