I'm reading selections from Inks and Paints of the Middle East: A Handbook of Abbasid Arts Technology by Joumana Medlej, which goes into great detail about the materials and techniques used to make paints during the Abbasid period. The focus is almost always on reconstructing how things were done at the time. Towards the beginning, however, there's a very sensible warning that many of these are toxic or harmful if inhaled, and you should take precautions like looking at an SDS and wearing a dust mask and gloves. This is the one section where the author doesn't give us any indication of how this relates to historical practice. Do we know anything about how artists and illuminators protected themselves from the risks associated with their craft?
I can't speak to the Arab tradition, but there is one mention from the Roman world which the Arab, East Roman, and Latin traditions grew out of. In book 33 of his Natural History, the Roman senator Pliny the Elder mentions the precautions used by workers who made red lead: "Those who grind red lead (minium) in workshops wrap their face with soft bladders, lest in breathing they should absorb dangerous dust and thus they look out over those (bladders)." None of the painters' manuals in Latin or the Romance languages which I have read mention anything specific among the people who used small quantities of these chemicals to paint things. You can also check Karen Larsdatter's page of paintings and prints of painters from the Latin Christian world to look for aprons and so on http://www.larsdatter.com/painting.htm
I don't think there is a lot of accessible material in European languages on Abbasid scribal practices other than the books by Joumana Medlej,.