After some messing about in the database, amusing myself and exploring things i'd never encountered, I noticed something not quite right.
While designing a ship, a particular pair of items are apparently inseparable. Selecting either will mount or remove both, simultaneously - getting only the one you chose is not possible.
So I did a little digging through the database to see if I can spot why, and I think I may have the answer.
Under ShipDesignComponents, item 65061 is listed twice, and the two items that hold that number are the inseparable pair in ship design.
Cross checking against TechSystem, noting the numbers they have there, and applying item # 26420 to one of the pair to match TechSystem seems to have corrected this.
A quick cross check of the stock database confirms the erroneous ID exists in the stock 7. 1 database.
I know 7. 1 is pretty much toast with c# really not all that far away now, but depending on how directly the data is carried across there is some risk this survived the transition unnoticed.