Once, I had a lot of tiny ships build before and that I do not want.
Instead of searching them and decommisionning one by one, I "sold" them to a minor faction.
I did not got a lot of money for them, but it was easy to spot them (they had a specific name) and it was just one click to offert them to the minor faction.
I assume it would work for ships coming from a faction that surrender to me.
Sorry for my English, I'm not a native speaker.