Who says IL-2 uses hit boxes? You can actually track every hit you've made exactly on which spot by using one of the game options in IL-2.
The problem with IL-2 DM is that the more sophisticated the DM becomes, the discrepancy between real life pilot reaction and us game pilot reactio begin to really show. For instance, many people still whine how .50s are undermodelled in IL-2, except from the receiving end the .50 does about as much damage as can be expected - instant flight surface/structural failures are very rare, but internal damage and flight destabilization being very common, and the no.1 killing factor when receiving .50 attacks tend to be black puffy engines and fires.
The thing is, real life pilots would not think twice about bugging out when they decide their rides are in no condition to fight any longer. They'd attempt to escape, and if even that seems unlikely, they'd just simply jump out. However, game pilots usually fight to the end until they drop dead. You could mess up a lot of internal systems on the plane, make it trail smoke, snag a control cable or two, shred a wing which starts drooping due to lack of lift, bust the oil pan to grease the entire windshield, hit the pilot so his vision goes all bloody red.... and yet, still the game pilot squirms and wobbles around trying to fight back.
It's because of this that its tougher to get kills with .50s in IL-2. The damage model's more realistic and sophisticated, but the pilots aren't. You have to keep stuffing in the .50s until the target is ablaze or loses a wing or a tail - and with the better DM, that's a tough objective to achieve without cannons.