I am not an expert on woocommerce… But Maybe I can try to help…
To get keywords with no result, an HTTP request must be sent to Matomo when the user uses the search feature of your website and there is no answer… (as an HTTP request is sent when there is some answers…)
Can you check this?
Also, how do you track searches within your application?
The wordpress matomo plugin is version 4.6. and the most recent matomo version is 4.10.1. When would next version for wordpress be available and would it be possible that it corrected this problem?