does my company use hazardous or harmful substances question

It's about hazard classes, not a feeling about the substance

Usually the question here is whether the company uses substances that fall under a recognized hazard classification — think of CLP classifications such as "hazardous to the aquatic environment", "carcinogenic" or "corrosive". So the question is not aimed at your own assessment, but at a factual check against the safety data sheet (SDS) of each substance the company purchases or processes. If the company does not use chemicals, solvents, cleaning agents in bulk or process auxiliaries, then "no" is often the correct answer — but verify this against the actual purchasing list, not against the intuition that "we are not a chemical company".

Doubt usually arises with small quantities: a can of degreaser, a battery, a circuit board with solder. VSME asks in the basic module mainly about the presence of hazardous substances and the way they are managed, not about an extensive life cycle analysis. If the answer dossier does not contain SDS's or a chemicals register, there is no source to support a "no" — then this field should remain open until someone internally has reviewed the purchasing list. This topic often also touches on the question of have the required environmental permits, because the use of hazardous substances above certain quantities may be subject to authorization requirements.

Where that is stated in the VSME base module

The basic module of EFRAG VSME includes hazardous substances as part of the environmental indicators alongside waste and emissions; see the source at EFRAG. This makes it a separate data point, separate from scope 1, 2 and 3 emissions from the GHG Protocol — a customer asking for the direct emissions of greenhouse gases does not automatically also ask about chemical use, even though both questions sometimes appear on the same page of the questionnaire.