If you were running at 3 knots you weren't "silent" they didn't have to ping you, they just had to drop depth charges on the only spot in the ocean making propeller noises.
Silent running just means stop all unnecessary noise (fans, pumps, giggling about playing grabass etc)
Silent speed on the other hand is anything under 50 revolutions... ie about 1 knot. At 3 knots in a VIIC you're cranking out 125 revolutions. More than enough swoosh swoosh sound to be picked up be passive sonar
You can run ahead flank at silent running... Or even ahead standard, but in doing so you're essentially just telling the crew to be quiet while you make as much noise as possible
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