Well, a sailor looking down from 15 or 20 meters high above the waterline in a large ship's command room will have far better chances of seeing your sub from afar than your lookouts sitting 2 meters above the water in the freezing cold. This is explained in the GWX manual. Your sub speed will also matter as a larger wake and splash created will make you more visible.
That being said, it sometimes happens that it takes a while for your crew to report a sighting, even if you can clearly see it yourself. I also find it interesting that the ship changed direction and ran away from you. Merchants usually just start zig-zagging but continue in the same direction, which makes intercept quite trivial in the end... Maybe it was just a coincidence?
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