The verb con probably stems from the verb conduct rather from another plausible precedent, the verb control (see http://dictionary.reference.com/browse/conning). It is noted that the conning tower allows for efficient reconnaissance.
On surface ships, the conning tower was a feature of all battleships and armored cruisers from about 1860 through World War I. Beginning in the late 1930s, as radar surpassed visual sighting as the primary method of detecting other ships, the conning tower was gradually replaced by a moderately armored conning station on the bridge.
In the Royal Navy, the conning tower was a massive structure reaching weights of hundreds of tons on the Admiral class battlecruiser (such as Hood) and as part of a massive armoured citadel (superstructure) on the mid-1920s Nelson-class battleships which had armour over a foot thick.
The United States Navy had mixed opinions of the conning tower, pointing out that its weight, high above the ship's center of gravity, did not contribute directly to fighting ability. Battleship designs before and during World War II began reducing or eliminating the conning tower. The Naval Battle of Guadalcanal briefly slowed this trend. When the Japanese battleship Kirishima hit South Dakota (BB-57) on the superstructure, many exposed crewmen were killed or wounded, but the captain, in the conning tower, survived the battle. Even that demonstration, however, did not halt the trend, and soon the heavy battleship conning towers were removed from USS Pennsylvania (BB-38), Tennessee (BB-43), California (BB-44), and West Virginia (BB-48), during their post-Pearl Harbor attack reconstructions and replaced with much lighter cruiser-style conning towers.
After World War II, as electronics began replacing the naked eye as the primary sensors, US ships were designed with expanded weather bridges enclosing the armored conning towers. On Iowa-class battleships, the conning tower is a vertical armor-plated cylinder with slit windows located in the middle of the bridge, climbing from deck 3 all the way up to the flying bridge on the O5.
The conning tower of a submarine was a small watertight compartment within her sail, from which the periscopes were used to direct the boat and launch torpedo attacks. It should not be confused with the submarine's control room, which was directly below it in the main pressure hull, or the bridge, a small exposed platform in the top of the sail. As improvements in technology allowed the periscopes to be made longer—then to be eliminated altogether, as in the Virginia-class—it became unnecessary to raise the conning station above the main pressure hull. The additional pressure hull was eliminated and the functions of the conning tower were added to the Command and Control Center. Thus it is incorrect to refer to the sail of a modern submarine as a conning tower.