I think that Okuda didn't keep a record of starships, where he had a listing of name, class, and registry for each ship. I think the Encyclopedia became this record. Even that official record is populated by mistakes, for example, a number of starships had two registries - Grissom
, and Zhukov
is an interesting case for me.
I think that Okuda remembered the name, but not its class, so now we have this situation where one starship has four registries.