I think there may be a point of interest regarding the diplomatic hit for capturing constructor ships. I've not looked in to it in my game terribly closely as I'm usually capturing pirate constructors and don't care about the rep hit.
That said, one does need to fire at the ship to drop any shields to capture it, so there should still be the same diplomatic hit as firing at it. However, is the same diplomatic hit levied for capturing the ship as is when destroying it? From the other empire's perspective, they lose control of the ship as assuredly as if it were destroyed, so I think it should be if isn't already.
Regarding the ship graveyards, I would assume the middling response to them on the part of the AI is a question of balance. If the AI were to treat them with the same priority as the player does, I would expect it would be faster about discovering and capitalizing them, resulting in quick leaps in AI tech and strength over the player. If that's true, then I would suggest that instead of having the AI respond tepidly, it send constructors to grab a few key ships and military ships to destroy the rest. If it can't have them, either because it couldn't afford to maintain them or because it doesn't have the time or resources to grab them, then it should work to deny them to everyone else by destroying them. Same goes for the world-destroyers.