I have hired a contractor and I am getting hardwood in my living room and tile in the kitchen. The contractor recommended that the shoe molding should be one color throughout both rooms even though the hardwood is dark chocolate and the tile will be beige.
Personally, I prefer any shoe molding to match the building's baseboards and trims, usually painted. I've had and seen many stained-to-match-the-floor shoe moldings and none ever appealed to me and always looked horrible. Painted means VERY much cheaper wood is used and the floor is now framed like the artwork it is.
Shoe Molding is ONLY to cover a gap between the floor and the wall, it shouldn't be in place if there's no gap to cover. Like, if the baseboard was done WRONG and placed on top of the finished floor or if there's wall-to-wall carpet, equals no shoe molding. And yes, if you go to a no-gap flooring in the future, the shoe molding should be removed.