As basic napkin math, if there's 1000 cargo ships moving in and out of the EU in a year, and this law adds 10 more. That's 1% increase. It's a bigger 1%, but I wouldn't be surprised if the emissions are less than the 9% of discarded clothes talked about in the article.
As you say, ships are moving in and out of the EU each year - the question is, how many have "back loads" - if some percentage of the ships leave Europe empty to return to Asia for more manufactured goods, then it seems very likely that they can have the containers of unwanted clothes as part of the trip.
Some of these arguments are so silly that I'm starting to understand why the EU thinks regulations are a free lunch to improve the environment with no costs whatsoever.
Airlines adjust capacity to demand — empty seats represent foregone revenue and future flights get cancelled or downsized.
Cargo ships don't work that way. A container ship returns to Asia whether it's carrying 1000 containers or 5000. The marginal emissions of an additional backload container are genuinely close to zero, not as a rhetorical trick but as a structural feature of how bulk shipping economics work.
If they would have flown the plane there anyway with an empty seat, your added CO2 is negligible yes.