
In 1970, before CGI, if you wanted to film it, you had to build it. By mistake rather than design, the ambitious Japanese set builders have given us Amagi as she would have appeared in 1941. IF Akagi's sister Amagi had not been wrecked in the Great Kanto earthquake of 1923, it is highly likely that she would have looked very much like the vessel shown in Tora Tora Tora. The higher number of landing accidents suffered by Akagi and Hiryu discouraged the continuation of this practice.

The reason for constructing Akagi and Hiryu with port-side command facilities was to enhance coordination between division mates in Japanese carrier forces. So the model and set don't match the real thing.

A picture of the real ship above a picture of the filming model: Now we can see plainly that the model and ergo the film set have their islands on the starboard side, unlike the real ship which was one of only two carriers with the island located on the port side.
