Hi Kristijan,
Can you please provide temporary back-end and FTP information so I can take a closer look at the issues? If the plugin is installed on the main site, and network activated, that should be it.
The only issue I can think of, is that maybe if the main site, where the plugin is configured does not have WooCommerce installed, then those specific custom post types may not show up on the back-end to choose from. It is a known issue, where on multisite networks it is not yet possible to list all the custom post types avaliable across the whole network. That should not stop the search itself though.
I’m afraid I need to see the configuration, as well as to be able to debug the code if needed to see if there is anything wrong. Thank you!