The most efficent/robust way is with the latest SubMenu (v3.7 at the very least has this feature), if you add the attribute "Do not display" with a value of 1, then the ship won't be shown in the menu.
For example the Akira:
import Foundation
setattr(Foundation.ShipDef.Akira, "Do not display", 1)
Or if you want the not so safe way, replace StaticDef.py with an empty file (or sans the ship definitions), but I honestly can't recommend that!