Most of the pictures I've seen of Japanese lines have overhead power. That lightning probably took down not only the train itself (yes, I understand the business about being inside the container - people inside would experience mainly a mental shock - but the same can't be said for the electrical gear) but also a chunk of the supply system (were some of those fireworks from melting wire?).

My comment about light rail trains is based on most of them in my area being quite old (nearing 30 years) and maintenance being not the best. Some (one I was on) have caught fire just running along without outside assistance.