The Germans have no destroyer present, therefore the defending air units can not hit the sub, and of course the sub can never hit planes. Think of it in terms of the combined arms rule, air units can only hit subs if they are combined with at least 1 participating destroyer, the difference with this particular combined arms is that it works while attacking and defending. In the scenario that you described, the sub would destroy the remaining transport without rolling and the defending fighters can do nothing.
Taranto question
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True, I did not mean to say that one bad-luck battle increases your odds of a future good-luck battle. What I meant is that Global 1940 is a much bigger game than, say, Revised. Global has more units involved and more battles that matter. The effect of having more units and more battles is to soften the effect of any one unit missing or of any one battle going poorly. In other words, as you broaden your sample size, you get closer to achieving average results in the aggregate.