I have the same problem with Avada theme, and I can’t find the main-cart-items.liquid or main-cart.liquid. Only cart.liquid, but the tracking doesn’t work.
If the cart-template.liquid file is missing in your Shopify theme, consider creating new create a custom cart template.
Go to the Sections folder, click “Add a new section,” and name it cart-template.liquid. Copy the necessary Matomo tracking code and insert it into the newly created file. For any further issue you might be consult with Shopify theme developer who can ensure that your cart template is properly integrated and tracking as expected.