I can't claim to know an awful lot about WWII fighter plane construction except for what I have seen personally, and the Goon restoration project that I have helped with a few times.
but...
What I DO know from those experiences and from scratch-building my own plane is that everything (obviously for weight purposes) is mostly hollow.
Wouldn't it seem that a round with more kinetic energy would have a tendency to pass through an airframe a lot easier, leaving less of an "exit wound", as opposed to, a round that was slower and perhaps would "tumble" leaving a bigger hole if it exited sideways, etc?
More surface area contact would transmit more of that kinetic energy (at least in theory).
I could be wrong. I THOUGHT I was wrong once, but it turned out that I was just mistaken... 
Well, if it's a skin-skin passthrough, it's barely going to transfer any KE. I'd think passthroughs would be roughly equivalent damage between them. Where the difference would occur would be hitting stuff that would offer more resistance, like the ribs on the wings, guns, gear, engines, armor plating and soforth. That's where you're going to see the difference between them.
I think Vinkman's point is probably right, that the DM assumes a projectile causes x amount of damage, and it's all transferred when it hits.
Now to drag myself back onto the tail thing and cannons and soforth. Question- from what I've seen of the damage ingame, it looks to me like there's no 'splash' damage from cannons. It looks to me like the individual round has to impact the part that it damages, is that right? I've never seen sprites on an elevator blow off a rudder, for example. I thought I saw somewhere that part of the modeling between cannons and MGs is that the cannons retain (possibly all) their damage out to further distances to simulate the explosive damage they have, while the MGs lose damage the further from the muzzle they go. Is that basically the difference between the two? It seems to me that's how it works. That would also explain only half of the tail getting blown off from the 30mm.
Personally I think that's a pretty fair representation until we can get the computing horsepower to get a DM that goes down to the rivet modeling deformation and damage. <g>
Wiley.