I'm new to GalCiv2 and the ship design stuff wasn't well explained in the tutorial. The game provides a number of basic ship designs as you discover new basic techs, but will those designs be automatically upgraded to the highest quality parts of each type as you discover new parts?
Nope. You have to go and upgrade these manually through the shipyard. Usually the prebuilt ship designs are just helpers to get you started. Some designs are unlocked if you research certain tech levels. Once you get familiar with the game you should be constantly updating your ship designs with the latest components as you progress through the tech tree. It is mostly advisable to build your own designs instead of relying on the prebuilt ones.
I've played many times, and I can certainly say that my warship designs get upgraded along with the availability of better weapons.
However, the upgrade didn't happen on every weapon upgrade, and it seems to consider only upgrades to weapons and defenses. No automatic implementation of better engines, for instance.
Plus, the newer designs seem to favor single-weapon-type warships.
So, it's always better to design one yourself.
And don't forget to use the "Obsolete" button on the older design after upgrading your ship design. It helps reducing the clutter in the shipbuilding dialog box. DO NOT use the same name; it will only confuse you horribly.