First, I don't consider myself to have been talking about professional fume extractors, more like what seem to me to likely be consumer ones.
elements of professional extractor.
1 Big and heavy filters containing lots of activated charcoal.
2 very powerful fan to draw air through 1
3 Date attached to filters after which must be replaced
Okay, that said.. and the following is important...
I don't know so much about this professional soldering station situation at all, and if one needs to know for health or especially regulatory reasons one should always be safe and ask whomever regulates workplace safety in their country (NIOSH or OSHA in the US, or perhaps ACOEM for air related things, also PubMed likely carries a lot of info if you learn how to use it.) I do know the British regulatory agency (I forget their name) has a publication specifically on colophony disease and allergy prevention. Thats where I would start.
What I was getting at is that in some consumer level "fume extractors" the activated charcoal is there for marketing purposes, primarily. They likely should not be used in businesses to offer worker protection. For the same reason one wouldn't wear a cheap procedure mask (worn by doctors in operating rooms and pedestrians on the streets of highly polluted cities to keep large dust particles out of their nose and mouth and contain their spittle by their face but not impede airflow too much) when one was performing mold remediation with known toxic mold. Or similar. You would use a NIOSH certified respirator and filter approved for use with that specific situation.
"Activated" carbon and some other similar materials are often used in filtration because of their huge surface areas at the microscopic level. Some filter materials leverage that surface which can be absolutely huge in terms of area, to clean air of toxic substances, with different materials having an ability, when fresh, to literally grab on to and hold a subset of substances which typically includes some dangerous ones. But there is no filter which will remove all dangerous substances, and some kinds of toxic substances which are in gaseous form are very difficult to remove.
Also, as you pointed out, the smaller a particle is the more likely it is to go deeply into the human lung and only the smallest particles (Lets say those of approximately one micron in size or smaller) typically make it to the portion of the lung where they can directly enter the bloodstream. Unfortunately, studies on some substances of great concern common in say, water damaged buildings, have shown that the smaller a dust particle in those environments is, is the far more likely dust filtered to remove particles above that size is to carry a high percentage by weight of those particular toxic substances. Whether that also applies in the context of soldering, (smaller size = more toxic) I have no idea. To be honest, I think the main risk of people working in electronics where rosin core solders are used is colophony disease. I dont know what the effect of overloading of a carbon filter is on its ability to filter out those particles. I think there is a good chance that at some point the filter becomes less of a sink than a delay line for such particles.
Activated charcoal comes with an ability to 'bind' certain kinds of molecules to its surface, which begins when the filter is opened and continues to be used up by contaminants of all kinds, we might think of it as a clock thats running even when the fan is not running and the "fume extractor" is stored away in a closet. All sorts of molecules, most of them benign use up that capacity.
So when the carbon has been exposed to the air for a fairly modest amount of time the filter no longer removes the kinds of polar molecules its designed to remove and to rejuvenate that capacity it would have to be heated up to a fairly high temperature in an oven which would send the contaminants back into the atmosphere, or replaced with a new one.