"The incandescent lights, including the spreader lights, were undamaged. "
LEDs are solid state devices and as such way easier to blow out. And from what little I can confirm, many of the LED "replacement" bulbs on the market have no surge protection, which is critical for a long life expectancy.
But even an incandescent bulb will blow out after running at 20VDC for a short while, and lightning can go way beyond that. It could be the LEDs were more susceptible to damage, or the stroke took a different path. Either way there's no question that good LEDs are way pricey--and, use much less power.
As Maine says...Only his LEDs were hit? Not all the electronics on the boat?