1. A container shipping company does not store the bar code of crates/packages. I've easily read 100s of booking details and never seen this. At most you maybe find one booking where the customer gave too much info and the customer service person copy/pasted too much. Anyway, either the article is talking about the container number or the hacked company is a logistics company.
2. If it is a logistics company, they wouldn't know exactly where the container is on the vessel. You can ask "above/below deck", but exact details aren't normally shared. You'd need to hack two companies if the pirates behaved like the article suggests.
3. Boarding a container ship isn't that easy as a lot of them are huge.
4. A container might just be reachable. Hint: For some commodities special care is taken to ensure that the vessel crew can still reach it. It's much easier to target a container after it has left a terminal and is e.g. on a truck. Note that even with full access it is better to somehow takeover a truck than to pick it up yourself; they check and your identification (passport/drivers license) when you pick up.
At most this might be about some logistics company that uses small vessels. E.g. intra Asia trade. Any big company I would be surprised if the hackers would make sense of all the systems :-P
That said, every so often you do see news articles whereby someone within either customs or a shipping company sells the details to others. Those others then steal the goods. But not by boarding vessels though, they takeover the truck.