As a professional engineer and a licensed amateur radio operator I have a little bit of insight on this subject so I couldent resist jumping in here.
If you were on the bridge and the lightning was to strike say a raised periscope or antenna your chances of surviving would be very very slim.
At best you would suffer perforated eardrums and severe burns. The conning tower would not act as a faraday cage in this case because the top is open. A faraday cage needs to be completly enclosed like... well a cage.
Also keep in mind that the crew would most like be wet not only wet but wet with salt water which is highly conductive making their feet a pretty damn good path to ground. Not a good thing.
Sailboats have their mast "grounded" in some cases and this provides some degree of protection. Also keep in mind a sailboats mast is considerably taller than a periscope and also has shrouds offering a vague form of farady cage sort of a tripod shape.
I have heard storys of folks clamping a set of jumper cables to their shrouds (wires that hold the mast up) and tossing the other end into the water to act as a ground.
In any case you had better unplug the radios... kill the electrical and stay as far away from any metallic objects on the boat. Something as simple as a metallic fire extinguisher can cause a "side flash".
As to the antenna being "grounded" .. not true the ocean itself in this case would be the ground plane and the antenna would be the radiating leg of a dipole antenna (the ungrounded leg). It may very well have a lightning arrestor or "blitz bug" in the feed line to protect the radio gear from discharges. The "blitz bug" (hopefully) diverts extreme currents into the ground plane instead of down the feedline and into the radio gear and possibly the radio operator.
The lightning would not actually have to strike the antenna to cause damage it would have to be just close enough to induce a current which can be quite a distance away.
I doubt that any Captian would elect to stay surfaced let alone keep a watch crew up there in a bad lightnnig storm. I know the sadistic bastard captins of this forum might
