I would see this question more in a global way. How is it with earth bounded vehicles and people in MP? Can they shoot up into the sky in any angle?
If yes, I say the flyers are build to fight ground troops, too. Everybody can shoot everybody.
But if anybody has a more qualified answer feel free to disagree 
Yes youīre right it should apply to all units that have a hindered firing arc.
Yes flyers are built for fighting ground troops but that doesnīt mean that they can do (and I think here of the other units with smaller firing Arcs, too) under all conditions.
Cars are made for driving, but you cant drive them up or down a wall.....
As most airplanes/-crafts arenīt thought for dipping the nose to fire with the weapons (except a StuKa) without losing their height.
But let me come to this in the reply to Enker.
Two options:
The simple one:
Let it all as it is.
There is no 3D Firing Arc and no real 3D Movement of a Flyer in Warzone.
Its only "quasi 3D" since you only change your height band and do not simulate ascending and descending in a real way,
with changing the noding arc, rotation arc etc. of the vehicle.
The result is, that there is no dead angle below a flyer.
The complex one:
You tranfer the firing arc into 3D with a dead angle below or above your vehicle.
But then you must also play flyers fully 3D.
This means you need rules for changing your pitch, roll, yaw angle.
You need rules for strafing. You nees rules for minimal movement and so on.
For me this is not playable in Warzone.
I think the first option isnīt logically right.
And the complex one is a bit too far fetched.....
But we could use the rules we already have!
Because there are actually rules for dead angles.
They refer to the fire trajectory of indirect fire, but could apply in a useful way here.
So a possible solution could be:
Minimum Range in inches to fire at the Target if having a hindered firing Arc (through MP, restrictet angles) [MRT] = height Band difference in inches [HBD] divided by the quotient of the normal firing Arc (normally 180°) and the actual (hindered) firing arc (normally 90°).
So that would mean for the standard case:
MRT = HBD / (180/90) --> MRT = HBD/2
BTW: We normally played with dead angles as you perhaps remember. Especially in the towers of the bridge field. And I think also with the aircontrol tower...