It is neither feasible nor practical to collect everything that comes out of a hydrocarbon-burning ship's exhaust. We have scrubbing for some of the worst stuff, but there's plenty of stuff that isn't collected.

When you burn fuel, you get a mix of those emissions. If burning fuel results in X amount of sulfur and Y amount of CO2, you still don't want to increase the amount of X, even if 100% of it is collected, because Y will also go up and it isn't being collected.