From a Nintendo Rep:

I was sorry to hear that you haven’t been able to locate a copy of Endless Ocean. Unfortunately, that game is no longer being published by Nintendo. As such, you might consider checking the secondhand video game market to see if you can locate a copy. This includes retail stores that deal in used games, pawn shops, garage sales, and auction websites.

This is a little odd, the first game sold pretty well, maybe Nintendo just wants people to focus on Endless Ocean 2. I don’t know?