This is a great question. I think the answer is probably that the energy in lightning is spread out over such a big area that it’s not enough to kill fish. Maybe if a fish got directly struck by lightning it wouldn’t do so well, but if it’s far away it probably wouldn’t feel any electric shock.
Water conducts electricity well: this is why you should never use a toaster in the bath (apart from the risk of soggy toast, of course!). But the electricity doesn’t move very far under the water: it’s easier for the electricity to move across the surface of the water. So unless fish are near the surface they won’t get hit by lightning.
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