Relston—
I am guessing that you didn't have a lightning grounding system on the boat. There are basically two schools of thought when it comes to lightning and boats.
The first school is that you bond the major metal elements of the boat together using heavy wire, and give the lightning as direct a path down to the water as possible. This, in theory, will create as simple a path for the lightning to travel, and not cause it to side flash. The side-flashes are what caused all the holes in your boat—and was the result of the lightning finding its own shortest paths to ground. In theory, this will protect the occupants, by creating a faraday cage of the stays, shrouds, mast, and rails. In theory, it will also help prevent side flashes. However, doing so will make the boat somewhat more likely to get hit by lightning.
The second school of thought on lightning, is to not bond the mast to the water. The idea here is that the boat will be less likely to be hit by lightning, since it isn't as good a ground as a bonded boat would be. However, the chances of serious damage, in the case of a lightning strike, are far greater, as you experienced.
The trade off is basically less severe damage and a slightly increased risk of being hit versus a greater risk of severe damage and a slightly lower chance of being hit.