I guess I'll have to change the story for my upcoming LDD representation the Dark Lightning. I guess the captain and crew will be removed ship service and placed under review for potential court marshal. Where is she currently berthed?
The Eslandolian Fleet seems to have suffered for the lack of the Dark Lightning. (She doesn't appear in the listing.) Dearji's blessing has apparently worn off.
I say that player captured ships do need to be represented with a new MOC, but if there is an existing full scale ship MOC, smaller representations (partial or micro) should be enough. If you wish to upgrade the captured ship, this should be a separate MOC afterwards.
The Dark Lightning is finished, but my mom's birthday delayed getting all the screenshots. She'll be up some time Monday, and I'll link the .lxf file if someone wants to do the rendering.