Hi,
To put an id on the invoice, you can edit the view "order / invoice" (backend template) via the menu Display > Views.
The user id is in the object $this->element.
In HikaShop we have an ID for the customers, this id is different than the Joomla ID.
So if you need the Joomla id you will probably have to call the function:
$userClass = hikashop_get('class.user');
$fullUser = $userClass->get($this->element->user_id);
$user_cms_id = $fullUser->user_cms_id;
You can display another id on the invoice if you want, but don't change the user id in database.