Is the amount of Christianity portrayed in anime representative of Japan? There are a large number of anime shows that portrays Christianity. Neon Genesis Evangelion shows a lot of Christian symbolism, such as crosses. Shows such as Trinity Cross and Chronos Crusade have nuns/people from the Church. Is the percentage of shows containing strongly Christian elements representative of the percentage of Christians in Japan?

I'm not expecting exact percentages, but more of a general ballpark idea.
No, not at all. As looper mentioned, the amount of Christianity in Japan is around 1% which is a really small percentage. 

Evangelion assistant director mentioned that they originally used Christian symbolism only to give the project a unique edge against other giant robot shows, and that it had no particular meaning:


  "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." source


This is the case in a lot of other anime series which have religious symbols: they are placed there to give the show a distinct look and feel, or to add a thin coat of mysticism.

Note the "we just thought the visual symbols of Christianity look cool" part of the above quote. I think (I may be wrong though, this is my personal opinion) that most of religious symbols in anime are there for that reason.