My answer:
At early technology stages, let the game design ships. After a while of that you are going to get to a point that you can equip a ship better than they do for your purposes.
I created one "this looks good to me" ship design without functioning parts for each hull size. When I am convinced the automatic designs aren't good enough, I pull up and upgrade the appropriate predesigned ship of the right size, throw in a bunch of engines, weapons and such, give it a name like 2-2 small attack so I know how big it is, and let that be the main ship for a while. Only after collecting a significant amount of further tech do I go in and upgrade the same or another blank ship again to get to something like 12-15 m attack.
This way, I design to my needs, but don't spend forever at the shipyards.
If I am being really lazy, I note that this method has left a whole lot of leftover designs with various ranking based names. I can just pick the highest one available and it tends to represent the same decisions I made before with the present tech choices available. That is an interesting shortcut.
If you build complex fleets of differing ship types, this won't be near as helpful.