I have auto-design turned on in my options so the computer pumps out new ship designs as new technology becomes available -- good time saver in some cases. I also have my options set so that when I click upgrade, the functional components are NOT removed.
What's interesting is when I upgraded a couple of the automatically-generated designs, the compuer had both over-filled the design (used 85 of 67 spaces) and had used a component that I had not yet researched (Plasma when my highest beam was Laser V).
Or do I misunderstand ship design?