1) Tilesets aren't small files. The process of even updating the tileset is something apparently Stefan frowns upon because of the process.
2) Levels aren't just made from tilesets. Many things are rendered as NPCs, but you can't really tell that because they use images that match the tileset. Changing the tileset(even making it darker) means all of those NPCs will suddenly not match the darkness of the tileset. This includes things like tree tops, roof tops, cave walls in some places.
3) Added onto the above, ALL npcs and players will stick out like sore thumbs. As the tileset is made darker to emulate a dark night, players and npcs will all be their regular shade, thus will be very bright against a dark tileset. This was a negative side-effect of the old backpal usage as well, where you could swap the palette of a tileset.