Silent running also stops all activities on the boat that makes noises, so when running on "Silent running"-mode, no flooding will be pumped away from flooding compartments in the U-boat, no torpedo-reloading is taking place, no repairs and no schnorkelling. All these activities were more or less noisy and i have experienced enemy DD's having an easy time finding me if they have caused flooding in some compartment for me. A couple of pumps running like crazy to eject all the flooding water must have made a lot of ruckus i think...
I have caught myself forgetting to "shut off" silent running sometimes, even after i have gotten rid of the enemies following me and i have surfaced and steamed away. "Enemy merchant spotted!" - SWEET!... But alas, i forgot to switch to "normal propulsion" and so, no torpedoes have been loaded on the entire day! Yet still the crew in the torpedo-room are utterly exhausted even though they haven't loaded any torpedoes. Guess the thought of reloading 4 torpedoes is enough to make you almost faint of exhaustion eh?