Bulbapedia: "This is a list of Pokémon by their color according to the Pokédex. While the actual colors of the Pokémon species can vary, the color listed in the Pokédex is usually the color most apparent or covering each Pokémon's body. No orange category exists; Pokémon that are primarily orange are listed as red or brown."
Pokemon are categorized by their most "apparent" colour according to the POKEDEX.
No, SHINY Pokemon are not included. That will be too complicated. I can't find any source that categorizes shiny sprites by colour.