I used to work at a steamship line, a competitor to MSC, at a US port office. The port terminals take security very seriously, but some of the steamship lines' offices are a bit lax. It doesn't surprise me at all that they were able to sneak in and install this equipment and malware, although I think social engineering (calling import customer service pretending to be the consignee and scamming them into giving you the pickup numbers) would be more effective.

Fascinating article though, and the story would make a good movie.