Well, in order to keep from having great huge armada's of mothballed ships waiting to be activated in a war....maybe you should be given a number of ships that could be mothballed without incurring a penalty, but if you go over that number...every ship afterward would cost a considerable percentage of what an active ship would cost to maintain. That, I think would deter/prevent you from having armada's just waiting to be called up....also, these ships would probably be obsolete any way, so they would only really be effective as a last ditch defense. You could also use this feature along with my idea for selling ships to other empires.....for instance you could sell ships out of your mothballed fleet. You could also conduct a 'lend/lease' effort to support your allly in battle by giving them some of your mothballed ships.
The idea of the construction ships is interesting and I understand it, however the idea I have in my head is that the ships would be decommissioned at a large dedicated Starbase or Depot on a planet or moon ( like the Zackdorn Quartermaster episode of TNG....which I looked up and watched this afternoon on You Tube...Thanks Igard and martok ). These facilities would have the equipment to strip them of their useful or 'dangerous' components.
"Tho' much is taken, much abides; and though we are not now that strength which in old days moved Earth and Heaven; that which we are, we are; One equal temper of heroic hearts, made weak by time and fate, but strong in will." -Tennyson