Here is the reason for the difference in the number of holes. See how the S-tune wing sits just above the third brake light.
Vs. the sport package wing, which sits over the third brake light. So it takes up more of the trunk. Those holes would probably be exposed if a S-Tune spoiler was in place.
The true Nismo wing also sits lower, which would cover those holes.
Evo-r or Seibon wings would sit over the brake light like a true Nismo wing.