Hi,
First, create a custom order field via the menu Display>Custom fields and turn off its "frontend" display option.
Then, in your plugin you can use such code:
$class = hikashop_get('class.order');
$order = new stdClass();
$order->order_id = $order_id;
$order->column = 'VALUE';
$class->save($order);
where column is the column name of your custom field and VALUE the value of the custom field.
Then, in the emails, you should be able to use such tag in order to display the value you entered in the custom field for your order:
{VAR:order.column}
where column is the column name of your custom field.