Why make the shipyard a separate program? You could give the shipyard an 'archive' button which moves the ship file to a folder which doesn't get loaded by the game at least as easily as making a separate program just for the shipyard function. The only value in having the shipyard as a separate program is that launching the shipyard would load a smaller portion of the game files than launching the full game would.
Additionally, while I am rather doubtful that you intended it as such, the way you worded your idea suggests that there would not be an in-game shipyard, which would naturally be a significant nuisance.
I can't say I'm particularly opposed to this, except in the case that the shipyard is removed from the actual game, but I don't really support it, either.