There's nothing surprising about large ships being more efficient. But a big issue is that many ships burn dirty fuel. Apparently there are no fuel standards in international waters.

As for the comparison to trains, it matters a lot whether you're talking about diesel or electric trains. Most train lines in Europe are electrified, and as electricity production switches to solar/wind, it may actually end up being cleaner than ships. (Although work is also being done on making ships cleaner. But new international laws are probably needed to get everybody on board.)

The real issue, though, isn't no much whether the transport happens by boat or train, but that it happens at all. The scale of global shipping is this big because everything is produced on the other side of the world. Big ships make that transport more efficient, but a more egalitarian global economy that didn't create incentives for companies to seek out every low-wage country and tax haven, would make local manufacturing more attractive and reduce global shipping.