Research completed.
Marks you get from hacking for an AI design: You get only the mark-Is, like the ARS. Overlaps with existing ship unlocks will be wasted.
ARS research if you already have the designs hacked elsewhere. Won't automatically grant you a new one (grants the first one when unhacked), so overlaps will be wasted. (Sucker.)
ARS hacking if you already have the potential designs hacked: unknown. I can't hack it due to having -747959.76 HaP.
Also...
1) I noted an interesting side-effect with the HaP accounting when hacking multiple ship designs. My Hap was 30 before this hack in a trivial testing game, and after hacking for 11 designs at once: -8519.76.
The correct accounting is done after the fact - since the next hack fatally chugs the game.
2) One AI's designs isn't necessarily stored on its own planets, but can be on the other AI's planets. I'm seeing two copies of some ships on 2x Everything AIs and this is probably the most likely explanation. These don't get coloured according to their target AI.