In and of themselves the hydrocarbons are molecules with only Carbon and Hydrogen atoms. So, they're polluting only in the sense that we should not release more Carbon Dioxide into our atmosphere because due to the Greenhouse Effect that causes Climate Disaster.

In terms of regular old "Oh, no, it's toxic" pollution this part was fine, and the problem in the "natural" hydrocarbons is that they were not actually pure hydrogen and carbon - especially coal. So you just wouldn't do that in the synthetics. It's likely easier to make "pure" synthetics.

In terms of climate, the synthetics would be cycling carbon that already exists. So they'd be neutral. Neutral isn't a solution, but it's at least not making the problem even worse which we are aggressively continuing to do as a species.

Because they would be generated with CO2 by industrial processes or carbon capture. I don't see the process becoming economically viable, and hydrocarbon combustion create other toxic byproducts, compared to hydrogen. It will still make sense for usages that require a high J/kg fuel ratio.