bhlaab: The reason is because there's no reason for them TO release it.
The only reason we have the source for Doom/Duke/Shadow Warrior is because id and 3D realms are... er, was in id's case... independent companies run by the developers. John Carmack is the kind of guy to say "Hey, why don't we release the Doom source code just because?" I doubt the head of Atari feels the same way about their library of intellectual property.
I'm actually glad you brought that up because its part of my point on an FPS thread in the General Discussion board. The mentality of companies was different back then because dev teams were, as you rightly point out, small, tight knit, and practically independent. Even though I think Duke's source wasn't released until sometime after 2000. Still, in Doom's case you're right. I just think that the story would be different if we were asking for the source to some FPS game from say 2000. One with fully polygonal 3D graphics...one that was intended to run in windows. But we're not. We're asking for a source that is extremely outdated and would only be used to port a game that is only now being officially reissued. I can't see how that would backfire. If anything it would generate more interest in the game. Yes, its their intellectual property. But, in terms of gaming technology, its like high school clay models versus post college relief sculpture. I can't see where they lose.