Yes, they will spot your scope. Keep your scope watches brief as you can. In calm seas expecially during the daytime they seem to spot your boat as well as a shadow in the water. Attack at night if you can.
As for manual targeting pratice try the short missions. They put you right on top of action. Once you go to manual targeting you'll never want to go back to auto. It is not 100% hits but the ones you do get are earned.
While you are on auto targeting watch closely the bow waves of your ships and note the speed. Later when you go to manual you will be able to tell better the speed by looking at the bow waves and the rooster tales thrown up by the props. This come sin handy should they spot you and change course or speed. Also study ship ID's as well.
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