But in this case with slow speed, it's the massive (literally) amount of mass of the cargo ship that gives it an un-intuitively large amount of energy.
To your point, it is mass. Most people don't understand mass on water. At 1 knot the ship would do the exact same damage, topple the support and drop the bridge.
Nitpick: squaring makes numbers greater than 1 bigger, and numbers smaller than 1 smaller. In this case we're squaring something with units, and we can't say the input is greater or smaller than the output, because they have different units. What we can say, is that v^2 curves upward: it grows faster with increasing v, and slower with decreasing v.
Reminder: Kinetic Energy = ½mv^2
Squaring numbers can make them big in a hurry.