I'm thinking that it had to shoot at
1of the 3 formations involved in the air assault on re-reading the overwatch rules right now- as overwatch fire happens immediatetely after the formation unloads troops (can't fire at the flyer moving because that would require AA fire) but before the assault has begun. Then I think, if that formation is wiped out, it isn't involved in the combined air assault (as it's wiped out before the point that the combined assault is engaged). However if you had shot at one of the assault marine squads and clipped off only two of the assault marines, then that formation would go into the assault with 3 blast markers, giving the combined assaulting army those 3 blast markers in the assault resolution. If you fired at and broke one of the assault marine units, they would break off and make their break move, then the thunderhawk and the other assault marine unit would then launch the assault.
So in summary I think overwatch shooting and the results of the shooting happen after the transport unloads, and before the assault happens, so at that point there are still multiple formations to hit? Then the results of the fire are applied to the target formation before the assault begins, so if they are destroyed or break they no longer are participants of the assault, but if they survive and take blast markers they participate in the assault and carry their blast markers into it?
Also on a related note, in my marine on marine game versus Gr00v3r, the T.O ruled that I wasn't allowed to scoop up my assault marines that had finished their action with my empty landing thunderhawk because he said they needed to contact the transport with an action- however that wasn't right, the units all just needed to be within 5cm of the lander to embark :-)