Seriously though, you got me curious now if there is a story behind this! OK, I found out it is from an old world english word cwen meaning regal woman or woman leader. Only unspayed breedable cats are 'queens', spayed cats are not.
Spayed female cats are called "spays" (or "speys") and neutered male cats are "gibs" (outdated) or "neuters", according to the MessyBeast website's Glossary of Basic Cat Terms. I also read somewhere else that "queen" only applies to a female cat who has become a mother. Intact female cats who have not had a litter yet are called "mollies," though I don't think most people know the difference with the terms. Nowadays, almost everyone who keeps cats as household pets get them spayed and neutered, so I have heard spays and neuters being referred to as queens and toms too.