When I score an event, the only credited "kills" are those actual and maneuver kills. If you crash, ditch, or anything else that does not give a kill to another player, it is not scored as a kill. I use the raw logs to score the events now exclusively. I can tell you whether or not a person landed all of his drones, but unless someone else got credited with a kill, I cannot tell you whether or not those drones he didn't land crashed, ditched, etc.; therefore, I do not credit them as kills for the oposing side.
We have tried scoring methods, in the past, that awarded folks that land safely. This was done in an attempt to reward life-like behavior and reduce the "gamey" techniques sometimes used with, for example, Kates when second lives are available. The results of these scoring techniques were inconclusive and created a huge burden on the CM scoring the event. I can tell you that tracking and awarding those points added at least an hour to an already 2-3 hour task for me. Ultimately, I decided it wasn't a cost effective method.
As far as the drone mechanics in-game--there's nothing we can do to change them. Formations in general are a valuable tool for the Admin CM, but certain setups allow us to turn them off if desired. Given that most bombers are pretty much nothing but flying targets with very little defensive capability, I enable formations in most of my setups, to ensure that those assigned bombers aren't getting clobbered early, and spending most of the Frame sitting in the tower listening to their buddies over voice. Early frame 1 I collided with some drones after popping the lead aircraft and it ended my night, so I can empathize with what you're saying.