I am not an HVAC guy but I deal with them in my job. It depends. They can theoretically get to all of it depending on your house and HVAC system layout. Will they? Maybe, maybe not. Would you be able to objectively tell without cutting into your ductwork? Probably not.
If I were to do it, I would have a highly rated and reputable HVAC service company do an examination of the whole system and take it from there. At the very least, they should remove the diffuser grilles and use a borescope to see how much accumulation you have.
Theoretically yes you could have additional "dust" in the residence if they clean it and something gets missed, like a loose or improperly sized filter.