Before 1911, hardly anybody knew that Machu Picchu existed which is why the Tomas thought it would be a great place to hide a clue. Even though many people know about this clue currently, the Tomas still have ways of protecting the clue. For example, planes are not allowed to fly over Machu Picchu so that other branches can't take photos.
Cocoa is mainly used to make chocolate even though cocoa is actually very bitter tasting. Cocoa originates as a bean.