How to change the HTML of the commerce shipping service form on checkout pages?
As suggested by clive, You should try this:

function MYMODULE_form_commerce_checkout_form_alter($form, &amp;$form_state, $form_id) {
  ...
}


or

function MYMODULE_form_alter($form, &amp;$form_state, $form_id) {
  switch ($form_id) {
    case 'commerce_checkout_form':
      ...
    break;
}