Magento 1.9 – Add New Category for Products with Special Price

user1618341,According magento an order can place from one store,Magento is save order store id at sales_flat_order,sales_flat_grid order.

At your collection you need get store_id.Also need rectify collection query,Please use * instead of some field

<?php
    try {
        $orders = Mage::getModel('sales/order')->getCollection()
            ->addFieldToFilter(
                'status',
                array(
                    'nin' => array('complete', 'canceled', 'processing', 'holded', 'fraud'),
                    'in' => 'pending',
                ))
            ->addAttributeToSelect('store_id')
            ->addAttributeToSelect('status');
    }
catch (Mage_Core_Exception $e) {
}

I have put the condition to skip create shipment for one store view[if($eachorder->getData('store_id')!=='YOUSKIPSTOREID'):]

see code:

try {

    foreach ($orders as $eachorder) {


        $order = Mage::getModel("sales/order")->load($eachorder->getId());
        if (!$order->canInvoice()) {
            Mage::throwException(Mage::helper('core')->__('Cannot create an invoice.'));
        }
        $invoice = Mage::getModel('sales/service_order', $order)->prepareInvoice();
        if (!$invoice->getTotalQty()) {
            Mage::throwException(Mage::helper('core')->__('Cannot create an invoice without products.'));
        }
        $invoice->setRequestedCaptureCase(Mage_Sales_Model_Order_Invoice::CAPTURE_ONLINE);
        $invoice->register();
        $transactionSave = Mage::getModel('core/resource_transaction')
            ->addObject($invoice)
            ->addObject($invoice->getOrder());
        $transactionSave->save();
        /* put code for skip for one store */
        if($eachorder->getData('store_id')!=='YOUSKIPSTOREID'):

            $shipment = $order->prepareShipment();

            if ($shipment) {
                $shipment->register();
                $order->setIsInProcess(true);

                $transaction_save = Mage::getModel('core/resource_transaction')
                    ->addObject($shipment)
                    ->addObject($shipment->getOrder())
                    ->save();
            } else {
                throw new Exception("Cant get shipment");
            }
        endif;

        $order->setState(Mage_Sales_Model_Order::STATE_COMPLETE);
        $order->save();
    }

}catch (Mage_Core_Exception $e) {

}

If you getting the issues for create invoice and shipment,Please see my Blog:

Create invoice:

Create Shipment:

In the observer, do you save the special price on the product?

For example:

$product->setSpecialPrice(123);

If so, then I would probably make a cronjob and run it each night. So every night you just run through all your products, if the price rules applies and are not already set, you just update the products special price and save it.

And if you want to run the script another time, just make a shell script and activate it that way at will.