I've known about the weird Ikana Castle paper airplane for a while. It may be a remnant of MM's beta stages, like a sidequest that was taken out at some point during the game's development. Oddly enough, they forgot to take the paper airplane model out. Maybe they used the deleted sidequest to test Bomber's Notebook functionality or something like that? Also, if there was such a sidequest, why was it removed? I'm also not sure if the paper airplane has any significance in the Japanese N64 version of MM either.
There are similar things in OoT, like an Arwing enemy that was coded into the game to test flying enemy AI. However, the code was never taken out, so with a cheating device (ex. Gameshark), you can actually fight the Arwing enemy!