I have to admit that's a good point I had not thought of before.
That my explain why, with my own son, his 2-seamer always registers at the same speeds as his 4-seamer, even though to my naked eye it looks like it comes in a tad slower.
Another issue is that often times, pitchers are trained to hold their 2-seamer off center -- fingers bunched on one seam to make it tail one way, on the other seam to make it run the other way. If the same amount of force is applied, but not through the center of the ball, the resulting forward velocity will be less than (as with the 4-seamer) when the force is applied directly through the ball's center of gravity.