The health effects of mold are not currently well documented. While about 30 species have been shown to have negative effects on the respiratory system, there are more than 250,000 unstudied species of mold/fungus on the planet.
We simply have not had enough time as a scientific community to completely understand what exposure does to a human being over time. That said, if you are experiencing symptoms as a result of even a minor amount of mold in the air, you should seek professional consultation to determine if a broad remediation of the issue is appropriate.
Regarding the chemicals used: most firms, if compliant with IICRC protocols and EPA standards, are using a fungicide that will not harm human beings. There is a list of EPA approved chemical compounds for use in residential settings. You can find this list online, or ask your contractor to produce the EPA registration number of the chemical in use if you have a specific worry.
Most contractors will also take the time to make sure surfaces are returned to a normal Ph level between 4–6 after remediation if a harsh chemical has been used. In the case of our firm, we use a green naturally-occurring solution that will not only kill mold chemically, but also mechanically break it down without any harsh additives.
It can be difficult to avoid some harsh chemical use depending on the nature of the mold and the cleanup required, so many contractors will also take the time to create a containment in the space which requires remediation.
Regardless of the situation, you’re allowed to ask questions of whoever you are working with. Most folks are happy to educate you, and while some contractors will simply say ‘its the way we have always done it,’ most people will know enough to tell you why.