The first Khaak Destroyer showed up in Ore Belt after I capped an empty Argon Mercury in Cloud Base South West.
The second showed up in Scale Plate Green after I capped an empty Teladi Vulture in Two Grand.
The third has shown up in Blue Profit after I capped a Paranid Perseus in Company Pride. Although it showed up when I was on the opposite side of the universe (Interworlds).
All empty ships start appearing after you have found the twelve listed on PCCenters spreadsheets. They will have weapons, shields, Jump drive and transporter devices installed with a few energy cells.
Also when you attack the Destroyer 6-7 super clusters arrive as back up.
I have decided to leave the remaining ships in situ for a later time.... when I've got an M1/M2 and a fair chance of winning without having to hide up the destroyers rear end.
D.