Yeah, though, on the bright side, if you don't care too much how the ship looks, its very easy to customize your ship. If you take the base ship you want and click the "use design" button, then you can double click on the defenses you don't want and they will go away and then double click on the defenses you do want and they will be automatically placed on the ship. It's still a pain because you'll have to go back in every time you tech up, but it's the best option until we get an in-game blueprint editor or some other way to easily modify the core ships or upgrade the custom ones.
