The best place to start would be with MSDS records for ITO and PET, then do some back-of-the-envelope estimates on exposure.
ITO itself is fairly inert, but can potentially break down into tin and indium oxides under heat. There are some health issues associated with long-term exposure to tin oxide, and indium oxide is known to be toxic. All heated plastics produce fumes that can be irritants to the eyes or respiratory system.
You have to consider dosages though.. PET is processed industrially by the ton, and the conditions in those factories have to meet OSHA standards. The amount of ITO on the surface of a sheet of plastic is probably in the milligram range (rounding up) and the amount volatized by laser cutting will be in the microgram range. Taking diffusion in air into account, we're into concentrations usually associated with homeopathy.
I'd say working in a room with decent ventilation would more than offset any chemical risks, especially if you aren't planning to cut the stuff eight hours a day for six months.
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