There's nothing in TF2 or Source's source code to indicate that knockback or air movement are affected by crouching.
For air resistance:
You can view the code for air movement here (CTFGameMovement::AirMove). You'll notice in CGameMovement::AirAccelerate that it applies friction while in the air from the pmove value m_surfaceFriction. That value doesn't change based on the duck state of the player meaning that there is no change in air resistance when ducking.
For knockback:
Knockback is a single "damage force" that is applied over a single frame on the server. You can see how its calculated here (CalculateBulletDamageForce). CalculateBulletDamageForce is called upon here by CTFPlayer::FireBullet - which is where hitscan weapons like Shotgun, Scattergun, Pistol, etc, process their the actual hit scan, damage, and damage force (knockback). Finally we can see where that calculated force is used to apply a single-tick impulse here.
Its fine to have preferences for gameplay; but, in the explicit scenario of getting denied by a scout while rocket jump, there is no clear difference between crouching and not crouching after rocket jumping. This is under the assumption that the scout has 100% accuracy and always hits you with a full damage meatshot.
ondkaja pointed something important out:
ondkajaStaying uncrouched while rocket jumping makes your hitbox 25% bigger, so it does make you easier to hit while in the air.
This is pretty accurate, and is somewhat effective in an attempt to reduce the amount of surface area the scout can damage. Since Scattergun's have spread, the scout has to get somewhat closer to you before they can hit you with all of the pellets in their shot.