Corrected entry: When Stapanak gets to the engine room you can see that the rocker arms are not moving, But yet they are moving fast up to the tanker. (01:11:50 - 01:12:20)
Question: Would pouring whiskey into the tank have really thinned down the mix, giving the submarine more speed?
Answer: Adding alcohol to gasoline can lower the fuel's viscosity, thinning it to flow more easily. It can only marginally increase an engine's speed and power.
But the question was, would it have actually increased the sub's speed?
Thinning the fuel mix would not increase energy or performance, so it would not make the submarine faster.
Technically, yes, diesel with alcohol burns better. As for what happened in the movie: no. Whiskey is not alcohol; it's water with alcohol, and the water reduces the flammability a lot. Also, a sub has fuel tanks that hold tens of thousands of gallons; adding a few ounces of whiskey will not have any effect at all.
Correction: When underwater Diesel/Electric Subs secure the diesel engines and run on their batteries and electric motors. Since the diesel engines are shut down, one would not expect the rocker arms to be moving.
Fun fact: those are not rocker arms; you're seeing the crankshaft. For some reason, they mounted the engine upside down, probably because it's easier to mock a crankshaft turning than a rocker arm assembly with valves and all that.