The Lightning Warhead is listed as causing AI progress +2 on detonation and this I observed as happening. As I understand it, if the DC is destroyed it should show in the hover-over that AI progress reduction is 20 and this didn't happen. Effective AI progress just stayed at the total figure (+2 for the warhead, of course) and I had no other reductions in play at the time.
If someone else has observed this, I'm going to conclude this is probably fairly consistent, whether a bug or not, and stick to raid starships and the like for long-range work unless there is some word one way or the other on it being by design or not.
Cheers,
Cos
PS. I am still enjoying the game very much and still in the early stages of learning strategies. I'm impressed by the adaptability of the AI.