Add value to a custom composite element in webform via hook_update_N
After trawling through the Webform source think I have an answer. 

/**
 * Update using hook_update_N for mymodule to add more options to a webform custom composite.
 */

function mymodule_update_8001() {

    . . .   

    // Update a composite element in a webform
    $webform = \Drupal::entityTypeManager()-&gt;getStorage('webform')-&gt;load('webform_id');
    $elements = $webform-&gt;getElementsDecodedAndFlattened();

    // Add new options here.
    $elements['my_composite_id']['#element']['my_composite_element_id']['#options']['my_new_option'] = 'My new option text';

    $webform-&gt;setElements($elements);
    $webform-&gt;save();

    . . .

}


Please let me know if there is a better way.