Yes, the destroyer in SZ 109 is why the fighters scrambling can hit your attacking submarines. You would have to hit in round 1 with your submarines and pray England does not get two hits in order to get that transport - that’s a risk I would not take.
Actually, if you are doing a SBR on England’s Airbase and succeed, England would not be able to scramble any planes into SZ109, 110 or 111, making an attack with only subs and few planes instead of many a very viable option. The only change I would suggest is hit SZ110 instead of SZ109. Also, your Germany Tac doesnt reach SZ111 unless you plan on building a Carrier.
All combat is simultanious. Unless that suddenly changed in Global 1940 - any damage you do to Air/Naval bases won’t take effect until after all your combats are resolved and you start Non-Combat.