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.
Do Subs Prohibit Loading of Escorted Transports
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Can a Trprt escorted by a DD move into a SZ with an enemy Sub during CombatMove and load the Trprt and continue on it’s way to conduct an Amphib attack ?
Or does the Sub make the SZ hostile preventing this ?
Thanks

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The answer is in the same paragraph you posted. A transport does not need any warships to LOAD a unit in Combat Movement. It just needs a warship to UNLOAD for an amphibious assault if there is a lone submarine present.
The key is the sea zone is friendly if there is just a submarine there when you loaded as per the last sentence below.

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