Why after her? Number One was only ever addressed as "Lieutenant", thereby quite possibly falling behind Elizabeth Dehner (who shared braid with people addressed as "Commander" or "Lieutenant Commander").
You're right. Pike had a crew of only 200 or so, which might imply fewer high ranking officers were aboard in those days. Number One was just a lieutenant even though she was second in command.
Pike himself, in theory, could have been a mere Star Fleet lieutenant in command of the ship, who was addressed as Captain because that's the custom and courtesy of these situations.