OK, the obvious 'duh' answer: because then you can use them in the next game.
That's great, but the next time I get to the point where I can build "nova 3's" (or whatever) I might have a better drive technology, which means that I could make the exact same ship, but with an extra pc/wk. Or I might have more miniaturization compared with when I initially designed the ship, and so I could cram more weapons/engines/range into the hull. So the "nova 3's" would be as bad as the pre-made ship designs. Given the way ship components miniaturize as they advance, it's unlikely that you'd want to build the *exact* same ship ever again. So what's the point in saving any ship from game to game? If I seriously kept all ship designs, in a few games I'd have dozens of incarnations of colony ships, constructors, fighters, etc, and most would be way underpowered for my current tech level. I've only played half a dozen or so games, so I'm pretty new to this still. Is there some aspect to ship design I'm completely missing?
On a slightly different note, as far as I can see, there's no way to take a design, and when my miniaturization gets better, start with that design as a template for an upgrade. This would make re-designing ships soooo much easier each time I get better drive/weapon/miniaturization technology. Does this exist and I'm simply not seeing it?