My apologies Felix for the flamers of Aces High. You have a valid question but it seems that the previous responses fail to address the real issues your question brings to light.
While the other post may be correct in noting the changes in the modeling, I sense your issue is how the stuka can be such a failure in AH. I dont know what your typical drop altitude is, but real life pilots came into their targets at much higher alts than the typical AH players.
In RL it was important to hit your target, but pilots were not usually in a situation were unduly risking the plane and pilot were secondary to hitting the target. Especially during the Stukas hay day. There would likely be more chances hit the target again. So I believe that drops were from higher alts than we typically see and the density of AA guns at the target was a factor. And if any pilot in real life dove so close to the ground as we do, it was most likely an error in judgement or an imperative need to hit the target.
This article
http://www.globalsecurity.org/military/systems/aircraft/sb.htm on the US scout bombers states "the aircraft was put into a vertical or near-vertical dive at an altitude 15 000 to 20 000 feet and aimed directly at the target. Bomb release usually took place at about 3000 feet, after which the aircraft made a high-g dive recovery..." I dont know the Stukas specifics, but I am sure it is similar.
Another issue at the heart of your question is AHs war format. As things are, without more cooperation between team mates in AH it is nearly impossible to employ bombers as they were in RL and survive to return to base.
In short, climb higher, drop higher, and try to put together highly organized and well executed missions for your Stuka.
Good Luck!