I definitely agree that all externalities should be paid for but the co2 emissions from shipping are very low compared to producing aluminium from coal. This comment puts it at 3%
Beginning January 2020 ships worldwide are required to burn fuel with less than 0.5% sulphur or install scrubbers, so the problem has been greatly reduced. It's still way worse than regular diesel, but it's much better (about where diesel was at 30 years ago).
https://news.ycombinator.com/item?id=23632148