Yes, when you turn off Silent Running auto-reload kicks in full swing. But don't use it when the DDs are pinging you. The reloading makes a lot of noise.
That's why when I attack a Task Force it's a one time shot. I go the periscope level make sure everything's ok. Set all forward torps to contact only between 7000-8000 yards away and fire all of them. Go to the deepest level I can get on Silent Running and sail away. Usually the DDs get close to me and the cat and mouse game begins. I realize also that Heavy Fog can be your best friend at times. DDs can't seem to find you.
DO NOT, I repeat, DO NOT TC WHEN ENEMY IS CLOSE BY. Made that mistake once and nearly bought the farm when a merchie deck gunned me.