If you are referring to the product categories widget, there is a setting to hide empty categories:

If you are referring to something else, please provide a URL to a sample page and the system status of your site. You can find it via WooCommerce > Status. Select Get System Report and then Copy for Support. Once completed, please paste it in your reply.

Hope this helps.

======Edit======

I think for the above problem you can use wc category hook and remove the category. Please check the code below:

//* 当小部件以下拉列表显示时使用
    add_filter( 'woocommerce_product_categories_widget_dropdown_args', 'rv_exclude_wc_widget_categories' );
    //* 当小部件以列表显示时使用
    add_filter( 'woocommerce_product_categories_widget_args', 'rv_exclude_wc_widget_categories' );
    function rv_exclude_wc_widget_categories( $cat_args ) {
    //添加逻辑来检查类别是否有产品，并创建ID数组，并用该数组替换下面的数组。
        $cat_args['exclude'] = array('55','68'); // 插入您希望排除的产品类别ID
        return $cat_args;
    }

In the above code, I think you can make the logic and check if the category has products and create an array of IDs for non-product categories.

This way you can exclude the category from lists and dropdowns.

Hope this helps.

With a lot of help from Harshit Vaid, I have successfully solved this problem:

add_filter( 'woocommerce_product_categories_widget_dropdown_args', 'eda_exclude_wc_widget_categories' );
add_filter( 'woocommerce_product_categories_widget_args', 'eda_exclude_wc_widget_categories' );

function eda_exclude_wc_widget_categories( $cat_args ) {

    $args = array(
        'taxonomy'   => 'product_cat',
        'hide_empty' => 0
    );

    $all_categories        = get_categories( $args );
    $category_exclude_list = array();

    foreach ( $all_categories as $cat ) {
        if ( $cat->category_parent == 0 ) {
            $category_id = $cat->term_id;

            $product_args = array(
                'posts_per_page' => - 1,
                'post_type'      => 'product',
                'tax_query'      => array(
                    array(
                        'taxonomy' => 'product_cat',
                        'terms'    => $category_id,
                        'field'    => 'term_id',
                        'operator' => 'IN'
                    )
                ),
                'meta_query'     => array(
                    array(
                        'key'   => '_eda_display_in_b2b',
                        'value' => 'yes'
                    )
                )
            );

            $query = new WP_Query( $product_args );
            $count = $query->post_count;

            if ( $count == 0 ) {
                array_push( $category_exclude_list, $category_id );
            }
        }
    }

    $cat_args['exclude'] = $category_exclude_list;

    return $cat_args;
}