Yes the sight height above the bore has to be taken into account. The down range trajectory or path of your bullet changes slighty with changes in the height of the scope/sight. Unless your are shooting tiny targets at long ranges in my opinion it's a moot thing.
For what it's worth I just ran these figures using a 7mm Nosler BT driven to 3450fps at ranges out to 1000 yds with sights 1 inch, 1 1/2 inch and 2 inches above the bore.
At 1000 yards the difference is only appx 9 inches with a 1 inch difference in sight height.
Of course with all computer ballistic programs I only use them as a guide, in actual shooting at these ranges the results will vary.
Pig Dog.... the bullet, no matter how fast it's drivenwhen fired from a firearm travels in an arch. Now imagine your eye sight is as staight line. When you are looking through a scope this imaginary straight line intersects the arch(path of bullet) twice. When you raise and lower the imaginary line(line of sight) through the arch it does change the amount ofelevation of the bullet at various distances. It's kind of hard for me to explain but in reality is quite simple.