I would also add that in real life, everyone involved was fighting for their life. Because of that, they were more careful in how they flew and fought as to minimize their risk. So, it would take more effort to shoot down a bomber.
And I believe you touched on the point that this is a game and it's more fun for people to be able to shoot down a plane (except for the one being shot down). The damage model in the WWII arena is a bit simple; no less than any other game of the genre and certainly better than some. The WWI arena is a testbed for the new damage model that you pointed out as being very much better. I believe I read that HTC will be implementing this new damage model for the WWII arenas over time as they shake out bugs and update the data for the WWII planes.