Things break and leak all the time, even on new ships. Automatic valves get stuck and things get clogged. I'm an air traffic controller now, and my break is over, but I'll try to expand more later.
Edit: I have a few minutes. A lot of people are talking about pirates only boarding ships to hold the crews hostage, and not to steal cargo. How about this: a pirate demands a crypto currency payment within X number of hours, or they sink the ship. It's very easy to sink a ship once you're inside.