I created a custom Types checkbox (show on frontpage) on WooCommerce categories.
I cannot set this field as a filter in my Taxonomy View where i list all WooCommerce categories.
I then thought i could just use conditional output to filter it out - but the Types custom checkbox field (show on frontpage) is not listed in the conditional output options.
From your post I gather that you are displaying a list of Woocommerce product categories using views, however you want to filter that list that is displayed with a query filter.
I recognise that the term custom fields do not show up in the GUI but you can add the information to the conditional manually.
All I did was to use the shortcode that I would normally use to display the field's value and then just add it to the conditional. In the conditional you see that i'm checking if the value is equal to 1. This is because on my backend the custom field value is set to 1 but the label is Show on Frontend.
That's what i did too after i posted this topic, and it worked for me.
I had bad experience using conditional fields from my previous topic with WooCommerce category images, and i thought that Views didn't support fields not in the GUI.