People have looked at the baseballs and can't figure out exactly what's different or the differences they do see would change the baseball so much, so there is room for alternative explanations. (Maybe all that motion sensor data, new coaching techniques, new types of PEDs, cork in the bats, all of the above).
Interesting. By my likely flawed logic, this seems like an answerable problem, mainly through investigating what you mention, and eliminating variables:
I haven't looked at the info, but I assume that if they know launch angle and the velocity (which I assume is right off the bat) and have this data for years, the question "Do the balls fly further" is easily answerable.
Then, I think the next question would be whether the energy transfer from the bat to the ball has changed, which would show up as higher exit velocities in the data. I assume that somewhere, they are measuring bat speed, and can reasonably conclude whether a change has occurred there (through coaching or technique). There's likely a variable about whether the "solidness of contact" has improved, but I would with enough data, some statistician can make conclusion on this variable with confidence. I suppose if they conclude there is something going on here, variables like corking or other bat changes might come into play and compete with improved techniques/coaching.
It seems like if they determine that balls aren't flying further, and that the transfer of energy into the ball is the same, it would simply be that the data set is now skewed to more advantageous launch angles.