I have found an exploitable bug that makes it easy to design super-ships. If you’ve had an event that give you a ship part that supposedly can only be used on one ship, here’s what to do:
* Design a ship with the single-use parts
* don’t build it
* build a similar ship (same size, preferably similar cost) and build it
* upgrade the ship you just built to the super-ship with single-use parts
* repeat last two steps as desired.
Rule the galaxy!