It's not necessary at all to identify properly a ship even in manual targeting. I use IABL's merchants fleet mod and there are so many ships that i sometimes make identification errors or simply cannot tell what is the ship inside my crosshairs. But after 7 years of playing i'm pretty good at estimating visually tonnage, range, speed and AOB so it's not a problem. Once the ship is sunk, go to your logbook and you will find what is the ship you sank even if you misidentified it first.
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