Hi mate!
Yes, weather was a factor in RL navigation (and has always been). Just watch "das boot", when the navigator tells the captain that he hasnt been able to get a good sun -or star "shot" because of the "sauer wetter". In real life they also use a timetable (dont know its name) to get the times right.
Edit: If they were near land, they could also use "dead-reconing", and use different land-base objects for recognition.
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