There's some subtext here and there it feels like, could be the yuri goggles. Zuikaku always talks about shoukaku as do others about sister ships or who've they've met before as the above stated.
^no. She first turned up before the Whateverth Impact that put Shinji out of the picture for years and stuck around as the whatchamacallem resistance groups other EVA pilot thereafter. Insofar the term remains applicable regarding the pilots the two aged together.
^ That's legitimate to have a prefered ship but that's not very nice to shame those who like another. We understand you don't like SayoHina but that's not a reason to call out those who like it.