I rarely use core designs, and usually obsolete them as soon as they show up. About the only exception is the default Colony, Constructor, Freightor & maybe Transport ships.
When I start a game with a new race (stock or custom), one of the first things I do is go into the Shipyard & redesign those core ships plus a Light Fighter (Tiny hull). The only things I add are the "bling" custom features; as I gain new hull sizes, I do the same for it. Then, as I upgrade drives, weapons & all else, I can update that prototype hull & re-save it as something different. I've also started deleting the older (but not the prototype!) models, so they don't clutter up the game. This lets me have a collection of "custom" ships, that I get access to immediately upon researching the base tech - hull size, trade & planetary invasion - without wondering what weapons or life support I also need. About the only thing I use the default ships for are some basic build ideas.
Now if the game would let me save different sets of ships into their own sub-folders.