Ships gained XP in GalCiv 2, but if I remember teh dev stream correctly, that system didn't really amount to anything useful in GalCiv 2, so it didn't make it into GalCiv 3. Instead there were plans to have commanders in fleets who would gain XP and that you would be able to swap experienced commanders around. However, as far as I know that didn't make it into the GalCiv 3 release version and will probably come as patch, dlc or expansion.