That is probably because that is how the shp file is organized. All of the borderlines with other countries and the sea are made into a polygon. The data associated with each of these boundaries has a country associated with it. That particular island in the South China Sea is a province of China in the shp file data. Thus removing all polygons associated with china includes Taiwan. The poster would have to go out of their way to modify the shp file to differentiate Taiwan from the rest of China to do what you said.