Why is my working Custom Taxonomy not in get_taxonomies array?

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The Invalid Taxonomy error will be raised by the function get_terms(). You’re registring your taxonomy on the init action hook. Therefore you have to call your get_terms() function on the same or a later hook.

Try this snippet. It should display all term names of your taxonomy, regardless if the term is empty.

add_action('init', 'wpse29164_registerTaxonomy');
function wpse29164_registerTaxonomy() {
    $args = array(
        'hierarchical' => true,
        'label' => 'Double IPAs',
        'show_ui' => true,
        'query_var' => true,
        'rewrite' => array(
            'slug' => 'double-ipa'
        ),
        'singular_label' => 'Double IPA'
    );

    register_taxonomy('double-ipa', array('post', 'page'), $args);

    $terms = get_terms('double-ipa', array('hide_empty' => false));
    foreach ($terms as $term) {
        echo $term->name;
    }
}

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