If you want to relive history, there is no German heavy bomber in widespread use outside of anti-shipping. You can point to 1,000 produced, but how many were in the air at any given time? How many were serviceable? Where did they serve? How did they fair against opposition? Why was production ended before the war ended?
If you want play balance the Germans (as part of the Axis) need a heavy bomber. That way if you want to draw the simple Axis/Allies line you have a bomber comparable to the the Allied's two heavies.
Really, you just need to decide what compromise you want to make.