I'm pretty sure that the Wilhelmshaven mod only changes harbors at the ports mentioned in the title. It puts gates into the locks in the Kiel Canal and those harbors. It doesn't affect the D-Day files at all. That will be strictly a GWX function, and if I remember correctly there are a lot of ships there. Possibly another mod is overwriting those files?
Use the Mission Editor to open the SH3 Map and look at the Normandy area. Every ship that appears any time during the war will be there, and you can see what's there and what isn't.
Also, why are you using version 5 when v.6 is so much better, and v.7 better still?
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