I just want to know if the goal scored by a player during shoot out is counted as goal scored in the tournament or not.
For example: the goal scored by Messi will be counted or not to become the highest goal scorer in the Fifa world cup.
No, it does not get counted. For instance, if we look at the goals scored by Messi during FIFA 2014 World cup: He has a total of 4 goals till now.
1 vs Bosnia and Herzegovina (group stage)
1 vs Iran (group stage)
2 vs Nigeria (group stage)
The statistics from FIFA summarize it the best.
First of all, Penalty Shootouts are different from Penaly Kicks.
Penalty Shootouts are played after the full 90 minutes & extra time. Penalty kicks scored here by the player will not be added to his goal tally.
Penalty Kicks are awarded by fouling an opposition player inside your penalty box. The goal scored by the player will be credited to him, because it inside the 90 minute play or the extra time.