Colony ships are one and done when setting up a new colony. The ship is used to build the colony's capital city. You can, however, use colony ships to shuttle population between two settled planets without having to destroy the ship. Max out the ship's cargo space when leaving one planet and then use only the minimum to leave the second.
As for transports, you should be able to reuse them now unless you are still using base game without the Crusaders DLC/Expansion.
