Ships and shaders are aesthetic. They should not take up space it our inventories.
Also, bungie will never create a ship or shader that looks exactly like you want it to, and if they did, it would be locked behind the RNG and you would likely never see it.
Solution: customizable ships and shaders. It makes more sense with the story's stretched resources.
The ship and shader rewards would be replaced with ship parts and shader colors. They would be unlocked on a list that is accessed while customizing.
This would help alleviate the inventory issues and make the game more personalizable.