There are several possibilities, Ackos.
First, did you design your ships under a different race? For example, you are playing a game as the Terrans and create some combat ships. Then you start a new game as the Yor and don't see them. This is because custom games are saved under that particular race. You can manually edit the files if you like. I know S0 is for the Terrans.
Second, you may have designed your ships in the campaign and now you are playing a custom game (or vice versa). You can go into your ship folders and move the design into the appropriate file.
Third, you may need more miniaturization. You can check this out in the research tree by looking up the weapon for the particular ship in interest and making sure it does *not* say, "more miniaturization needed."
Fourth, you might be forgetting another component you have to research like an engine, for example.
Hope this helps!