codeigniter active record left join

You have wrong where clause you need to compare user_id from your table ,you are comparing the id of email to the provided $user_id

$CI->db->select('email');
$CI->db->from('emails');
$CI->db->where('user_id', $userid);
$CI->db->join('user_email', 'user_email.user_id = emails.id', 'left');
$query = $CI->db->get(); 

A more useful way is to give aliases to your tables so the tables with same columns will not have any confusion

$CI->db->select('e.email');
$CI->db->from('emails e');
$CI->db->join('user_email ue', 'ue.user_id = e.id', 'left');
$CI->db->where('ue.user_id', $userid);
$query = $CI->db->get();