Figured it out myself. Apparently, the pagination break because both my ‘products’ and my ‘types’ (those are not the terms I have, just for demonstration purposes) are having the same slug. Products has a slug of ‘products’ and types has a slug of ‘products/%typename%’. Due to this I can make my permalinks hierarchical: products/dvd or products/cd. It worked, although, it broke both my pagination on taxonomy archive-pages as it broke my permalinks to individual post-types. What I did was the following to fix it:
function add_rewrite_rules($rules) {
$newrules['([^/]+)/([^\.]+).html$'] = 'index.php?$matches[1]=$matches[2]';
$newrules['([^/]+)/([^/]+)/page/?([0-9]{1,})/?$'] = 'index.php?post_type=$matches[1]&locations=$matches[2]&paged=$matches[3]';
$rules = $newrules + $rules;
return $rules;
}
add_filter('rewrite_rules_array', 'add_rewrite_rules');
I added some mod-rewrite rules so apache will find the paginated taxonomy archive and the individual archive-post.