The question is quite clear. Also, I have been asking around this question for long and I have been getting mixed responses. Some say it is counted as the first bouncer for the over and others don't believe that they are counted as one-above-the-shoulder. So it will be good if the answer is somewhat official - taken from the rule's book.
As per ICC's standard ODI match playing conditions PDF, law 42.4.1 states that:
... d) ...a ball that passes above head height of the batsman, that prevents him from being able to hit it with his bat by means of a normal cricket stroke shall be called a wide.
e) For the avoidance of doubt any fast short pitched delivery that is called a wide under this playing condition shall also count as one of the allowable short pitched deliveries in that over.
So, the answer is YES. It will be counted as one over the shoulder.
The leg side wide which has been bowled over the head of the batsman is not considered as one-over-the-shoulder for the following reasons
- For umpire to warn the bowler as one-over-the-shoulder the ball should be bowled to the batsman body which makes it as a dangerous ball.
- Here in this case ball has been bowled leg-side so no its not going to do any damage to batsmen to consider it as a dangerous ball more-over most of the times it will be accounted as a wide for bowling leg-side rather than considering it as a wide for going over the top of the head.
As far as I have seen, there are no specific rules mentioning this case. Some matches I have seen umpire calling it as just wide and some cases, it is also called as over the shoulder too. So the answer is it depends on the umpire, just like how LBW is called when player steps out of the crease.