Short Answer: The error is generated due to a missing mod (The Ship Addon for Unity if memory serves). to resolve the issue either re-enable the mod or remove the ship designs that are in error and your good to go.
Long Answer: When the game starts it loads up all your ships. If the game can not find a hull, module, weapon etc for that ship the game will not load.
to solve this you need to either:
- Re-enable the mod which has the missing module/ship (in this case its the Ship Addon pack for the Unity Mod)
- Remove the ship designs that are using modules/hulls that no longer exist. (you will have to head to \Documents\My Games\GratuitousSpaceBattles\ships)
- reinstall the mod - the Zephyrus Cruiser was a Addon for the Unity Mod.