Getting struck by lighting...

[Panser]

For the most part a U-boat being struck by lightning would have a similar effect to a Faraday cage whereby the discharge of lightning would most likely pass through the outer hull and down through the keel into the sea. No doubt there would be a strong likelihood of damage to internal systems and quite possibly a hair raising experience for all within.

As Jim said the watch crew would potentially be in danger, though in the heavy seas that would usually accompany such a storm the boat would be constantly pitching and rolling. At any particular moment the bow, the stern or even something like the DF loop could be the highest point available to a lightning strike.