A scout swarm shouldn't stop a nuke because the nuke should be big/heavy enough to punch through it. Allowing scouts and other T1-T3 aircraft to stop a nuke is therefore bad. It's not "REAL LIFE LORE" to let people block nukes with paper planes.
I think artillery can hit air units (look at people blocking mavor shots with t2 transports). I think light arty and fatboys don't shoot high enough to hit most air units (although if there are extreme differences in elevation, perhaps they would be able to hit). And I have seen people ground-fire artillery to try to hit a Czar. I think I've seen people ground-fire a scathis to try to hit flying ASFs. (Speaking of ridiculousness, an ASF can absorb a full scathis shot without dying o_O)
If t1 bomber planes were drawn in-game as "low" enough to the ground to run into shots from weapons platforms like t1 light arty and fatboys, we would have to ask: why?
Are they drawn as being low to the ground because attack bombers are low-flying units that have to brave enemy ground fire in order to deliver their payload? In which case, they should collide with those weapons and take damage because that is what is intended. OR, are they drawn as being low to the ground because of engine limitations or some other arbitrary reason that has no connection to what the unit is, in an abstract way, supposed to represent? If it's the latter, then there should be no collisions. Either the bombers should be drawn higher, so they can't collide (and so their visual representation in the game matches what they are, in an ideal/abstract sense, supposed to represent), or at least as a workaround those projectiles should pass harmlessly through them without colliding.
It might be interesting if units could "ground fire" to an arbitrary height (as in: ground fire at this spot, but pretend like there's a really high mountain there, so actually you're shooting into the air) in order to let ground units damage things like Soul Rippers and Czars. Interesting, sure, and it would reward micro, but would it improve the game? I think the answer is "no," just like it would not improve the game to allow flak and SAMS to ground-fire against ground units.