No one ever travelled in a decks awash condition. As you point out, it causes complications with drag and fuel usage. What is being said is that it was used a lot for night surface attacks. You want to be moving slowly to keep wake and phosphorescence down, and the lower profile helps when approaching enemy shipping, and you're already at or near neutral bouyancy which helps you get down faster if you are spotted.
The game doesn't reflect the procedure properly. I'm pretty sure that most decks-awash attacks were conducted on battery power, to help keep noise down. In the game that automatically makes you 'submerged', so the watch crew disappears. The lowered 'surface' depth is the only compromise available.
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