I think it's less a matter of preferring to launch with E9s, and more a matter of building for flexibility. If you build a rocket with a 3.75" motor mount, you can fly both E9s and D12s (with a 1" adapter) in your rocket. On the other hand, if you put a 2.75" mount in the rocket, you can ONLY fly it on D12s (or, of course, C11s). So it makes sense to put the longer mount in rocket that you might want to fly on Es.
Also consider that, with the standard unmodified Estes 2.75" motor hook, you cannot fly Aerotech 24mm motors in the rocket - the top of the motor hook is too long and the Aerotech motor won't fit. However, an Aerotech motor WILL work with the orange spacer and a standard unmodified 3.75" motor hook - the ejection cap fits fine inside the spacer and the spacer engages the top of the motor hook. So if you build a model with a 2.75" motor mount and don't modify the motor hook (you need to remove about 1/8" or so of the top of the hook), you can't even fly Aerotech Ds and Es in the model.
So, I think it is more a matter of flexibility than any real preference for one over the other. BUT - that is only my opinion. I could easily be wrong.