You cannot have more than one of your purchased C-Store ships on one character. I think that is a pity.
Most ships have a number of skins and you can also make different configurations with weapons, consoles and BOFFs. Since you can only play with one character and have only one ship active (the ship is actually your character with a special skin), I don't think it would be a bad thing if we could have more than one of your purchased ships on a character.
Anyway, even if you want to spend Zen to buy a second copy, it isn't possible. Not that I am interested in that option though.