Magento 1.9 – How to Get Root Category Details

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:

Modified method getCacheKeyInfo in class Mage_Page_Block_Html_Topmenu as below

public function getCacheKeyInfo()
    {
        $shortCacheId = array(
            'TOPMENU',
            Mage::app()->getStore()->getId(),
            (int)Mage::app()->getStore()->isCurrentlySecure(), // newly added line to check if secure or non secure
            Mage::getDesign()->getPackageName(),
            Mage::getDesign()->getTheme('template'),
            Mage::getSingleton('customer/session')->getCustomerGroupId(),
            'template' => $this->getTemplate(),
            'name' => $this->getNameInLayout(),
            $this->getCurrentEntityKey()
        );
        $cacheId = $shortCacheId;

        $shortCacheId = array_values($shortCacheId);
        $shortCacheId = implode('|', $shortCacheId);
        $shortCacheId = md5($shortCacheId);

        $cacheId['entity_key'] = $this->getCurrentEntityKey();
        $cacheId['short_cache_id'] = $shortCacheId;

        return $cacheId;
    }