The Drej is an A.I.

Just think of the Drej as Gort made of energy but somehow they got out of control and over stepped their original programming

I don't know about the Drej being an A.I. makes me think of that one Futurama episode were the Professor created some kind of nanobots that evolve on a planet each day until they evolved beyond their physical forms.

But that could be true about the Drej, but I always thought of them as a race like the Vorlons and the Shadows and other First Ones from Babylon 5, they were around for Eons that they evolved from their physical form into a pure energy based form like the First Ones did.

As for that spare Drej fighter in the cargo bay of the Valkeryie that you think might regenerate the whole Drej race, I doubt it's still there, Korso must've disintegrated that thing and I doubt that one fighter could respawn all of the Drej.

But another way I can think of were the Drej can be reborn and make a comeback as a whole is if you read the prequel comics before Earth was destroyed with young Korso and Sam, there was a Drej artifact that was mentioned in the comics called the Orb. Believe it or not, the Queen Drej was not the only Mother Drej in the past. There were two other Mother Drej with her that kinda formed a royal family sort of speak, there was a King Drej and a Prince Drej that ruled along side her in a power circle. The Orb is said to shape the destiny and will of the entire Drej race, all three of them controlled the vast army of Drones using the Orb making them the Hive minds, but the King and Prince were domestically fighting amongst each other and caused the Drones to be in a disarray making them lose plenty of battles to the humans and other races that fought against them. The Queen stuck in the middle was frustrated with the both of them that she took it upon herself to be the sole ruler of the Drej Empire and killed both the King and Prince when they were weaken by absorbing their energy into her own, afterwards she controlled the Orb by herself.

So maybe the Orb survived the disintegration of the Drej Mothership and will probably be the thing that regerates the whole Drej race.

As for the Drej's motives for Destroying the Earth and trying to wipe out all of Humanity. Well it could be the Drej wanted to remain the dominate race in the Galaxy and felt threaten by the human's creativity or they didn't want the humans to evolve more and threaten their dominance. They mention a few things here on this link that sheds a little light on the Drej's motives and maybe their orgin http://www.adherents.com/lit/Na/Na_177.html . Another source in the comics also states that the Drej destroy planets so they can re energize themselves from the energy of a destroyed planet.

Policing for their own ends.... To keep on the to; of the food chain