Is there any reason the ship designs are not researched the same way the missile design are? It would solve a lot of weird behavior associated with modifying a ship design while it is still in service... It also mean the design decision are more meaningful as they cannot be instantly modified.
I believe that this is encompassed in the retooling costs, which grow bigger the larger the change you make in terms of design cost. In other words, my understanding is that part of the cost of retooling is in the R&D of working out the kinks in the design. Before retooling, it was as you said - a ship could be designed and construction upon it started in zero game time. My recollection is that the reason Steve put retooling in was precisely to address your concerns - that it was too easy (quick) to begin production on a new design. You might try looking/searching in the Mechanics board for the retooling shipyards discussion (it might be jumbled up with the slipways discussion) if you're interested in reading about the debate - not sure if the discussion was before or after our most recent loss-of-old-posts.
I'd also like to reiterate that modifying a ship design while it's in service is not playing the game as it's intended to be played (i.e. locking designs before retooling/building and not changing locked designs). If you play as intended, then a new ship design cannot be instantly be put into production - in fact it can often take a year or more simply to get the SY retooled. For example, I just designed a large civie freighter (10 holds, 80kton). Simply retooling the SY is going to take me more than a year of game time. After that, I suspect that the first ship will take a year or two to construct (assuming that I don't prefab some civie engines with my industry). So it can take several years to get the lead ship in a new class of freighter built. And once the retool is started I'm stuck with it - if I realize I made a design error I need to wait for the retool for finish, then launch another retool to get to the design I want (as long as I play the game as intended).
John