You're right that not all aspects of Article 9.1(a) make sense for SaMD-IVDs, but it's generally not correct to mark the entire requirement as 'not applicable' just because the product is software. Instead, you should review each aspect (e.g., trueness, precision, accuracy, limits of detection) and indicate which ones make sense for your particular software. For example, precision and accuracy often do apply, while analytical sensitivity might not.
It's good practice to mark the requirement as applicable, then add comments or notes in your GSPR explaining which parts are relevant and how you address them. For the aspects that aren't applicable, provide a brief justification. This approach shows that you've considered each requirement carefully and have a rationale for your conclusions.