Why are crosses so popular in anime and manga?
One possible explanation could be that it looks foriegn or exotic, or "western". In Neon Genesis Evangelion, which uses the cross symbol pretty rampantly, one of the creators gave this explanation (from the Q&amp;A "Amusing Himself to Death" with Tsurumaki):


  Can you explain the symbolism of the cross in Evangelion?
  
  KT: There are a lot of giant robot shows in Japan, and we did want our story to have a religious theme to help distinguish us. Because Christianity is an uncommon religion in Japan we thought it would be mysterious. None of the staff who worked on Eva are Christians. There is no actual Christian meaning to the show, we just thought the visual symbols of Christianity look cool. If we had known the show would get distributed in the US and Europe we might have rethought that choice. 


(Emphasis is mine)

So it may not be that the cross means something different in Japan (most weddings take place in a Christian church, I believe), but that because it has an air of the exotic or mysterious.