You are not wrong regarding reasons why digging was made harder for aviation archaeology. But, licenses can be applied for, if there are sufficient qualifications and understanding of the archaeology, as opposed to 'just' digging it up. Certain wrecks may be identifed as to their rarity, i.e., being the only one left, protype, therefore an argument can be made as to its recovery. The Dornier 17 recently identified on the goodwin sands is a good example of that.
And if you look at how bad the Time Team recovery of an Invader in Preston was, there is scope for good archaeology.