This isn't a force play, so the batter is out either when he is tagged out or when the ball reaches the base.
If there were runners behind that would otherwise score, then per 5.09(d), they could not score if the runner ahead made the third out on appeal. But in your scenario, there are no runners behind the play.
So all 3 preceding runners score. The third out happened after they reached home. If the defense noticed the miss immediately and threw to second rather than to try to tag someone at home, then it would depend on the timing of when the base is tagged and when the runners reach home. Only the runners reaching the plate prior to the third out can score.