Remove Home from menu at module installation
Following the suggestion from @Leigh Mason and copying almost verbatim from the link he posted, I ended up implementing hook_install():

function hook_install() {
  $menu_link_manager = \Drupal::service('plugin.manager.menu.link') ;
  $front_page_link = $menu_link_manager-&gt;getDefinition('standard.front_page') ;
  $front_page_link['enabled'] = 0 ;
  $menu_link_manager-&gt;updateDefinition($menu_id, $front_page_link) ;
  $cache = \Drupal::cache('menu') ;
  $cache-&gt;deleteAll() ;
}


and the link was successfully deleted. I think that the last two lines are not really needed, I will check it at the next build from scratch...