Yes you can upgrade your ships. In Gal Civ III this was called retrofitting.
Example You create your own small hull that has basic lasers and all three defenses, call it 'laser boat'.
Later you research disrupters and better defenses and a shiny new engine upgrade.
You go back into your designs, use the existing design, upgrade with new parts and call it 'laser boat 2'.
Now, HOW DO YOU UPGRADE IN GAME? Funny you ask. I found out only via the discord when another old player showed me.
You must create a way point in game with any ship. Drive your ship you want to upgrade on it, if there is still movement left you can click on that ship and you will see an UPGRADE ARROW, click this and you will have a pop up that lists what that ship can upgrade to and it includes designs you made!
This was my biggest peeve and its is back. While its clunky and only one ship at a time I will be just happy with it!
Hope this helps.