A very long, well written Von Neumann theory on page 3.
<joke>I've got it! There were two races before the Ancients. One who built the Shivans (Let's call them "M"), and another with a lust for knowledge (Let's call them "S"). The S purchased a liscense to use the Shivan technology from the M for use as an advanced scout program. Unfortunately, the guy in charge of the Shivan scout project set the priority for self-replication a little too high. Shortly therafter, he lost the slip of paper that he wrote the self destruct code on.
Then the Shivans get out of hand with their self-replication and kill everyone.
</joke>
(I like the second part of your theory)
Seriously though, I have a half thought out theory:
So the Shivans are really old, and they kill pretty much everyone they come in contact with. Sometime before they killed the Ancients, they became whatever type of hive mind. And then in all that time, they just leisurly build ships, explore the universe, philosophize, and become intimately familiar with subspace. Ancients show up and start causing havoc, using subspace a lot to spread that havoc.
See, the Shivans have become rather possessive of subspace itself in all those millenia. When somebody else shows up and starts messing with it, the Shivans react negatively, becoming absolutely focused on destroying them. Maybe it was the construction of the Knossos portals that bugged the Shivans.
So, another *very long* time passes, during which the Shivans continue to build and expand. They have no enemies and therefore no reason to build new technology.
Eventually two more races appear. They're both using subspace to fight eachother, and not treating it very well. Shivans are all, "Can't let you do that, new guys," and send the Lucifer fleet to teach them a lesson they won't survive to learn from.
To their surprise, these two races are far more adaptable and resiliant than expected and they actually beat the Lucifer.
Shivans decide that they'll need a different plan this time. For the first time in millenia they need to think originally and make strategies and new weapons. BAM! Lucifer beams for everyship! BOOM! New fighters and bombers! POW! Send in the Sathanas(es)! WHOOMPH! Blow up a star! That'll teach 'em.
Also to their surprise, instead of dying or fleeing, one guy decides that he want's to try to talk to the Shivans. They don't remember any non-killing form of contact with any other race ever, so they are intrigued. 'Course, the rest of the upstart species still need their spanking.
The theories about shipyard/carrier/battleships are good too, they make sense.
EDITed for readability.