There is some debate as to why a 2 seam fastball tends to be slower than a 4 seam fastball. Most believe that having more seams spinning reduces the drag. However, some studies have shown analytically that there shouldn't be any significant change in the drag coefficient between a 2 seam and a 4 seam fastball.
In any case, velocity measurements are usually taken at a point very close to release where the aerodynamics haven't had a chance to make much difference at all so there shouldn't be any difference in the release velocity of a 2 seamer and a 4 seamer unless pitchers simply don't try to throw 2 seamers as hard.
It would be interesting to gun a large group of pitchers throwing 2 seam and 4 seam fastballs, measuring velocities at release and at the plate to see if there's a difference in how much a 2 seamer slows from release to the plate compared to how much a 4 seamer slows. At the same time the 2 seam vs. 4 seam release velocities could be compared. This should be enough to determine if the velocity difference exists, and if there is an aerodynamic effect.