I think the same conventions that affected civilian ships also affected civilian aircraft, and the same attitude by the bellligerents i.e. ships/aircraft, even though civilian in that they do not carry defensive or offensive weapons, are assumed to be part of the war effort of said country and so fair game for attack. The only exceptions being craft from neutral countries amd they should be explicially marked as such.
There appear to be no explicit treaties/concentions of war that mention civilian aircraft but I have read that aircraft were treated in the same way as ships when retrospectively judging legality of action.
http://avalon.law.yale.edu/subject_menus/lawwar.asp