Sure, easy: Data/Cfg/GameplaySettings.cfg. At the bottom see:
[MiscSettings]
AlwaysAutotargeting=0,0,0,0,0;for warships, merchants, uboats, air and land targets
Re-number the zeros for the default actions:
1 = Maintain current orders.
2 = Engage target.
3 = Periscope Depth.
I'm not 100% sure about the last two, but you get the idea. I have everything set to '1', which prevents the window from ever appearing or any new orders being issued.
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