The Zen Cart order-confirmation email is sent via the store-side order class' send_order_email function.
You can modify your store to not send the email during checkout by editing your template's override of /includes/modules/checkout_process.php (the copy of that file that is present in /includes/modules/YOUR_TEMPLATE/checkout_process.php) and commenting-out the call to send_order_email:
Code:
// load the before_process function from the payment modules
$payment_modules->before_process();
$zco_notifier->notify('NOTIFY_CHECKOUT_PROCESS_AFTER_PAYMENT_MODULES_BEFOREPROCESS');
// create the order record
$insert_id = $order->create($order_totals, 2);
$zco_notifier->notify('NOTIFY_CHECKOUT_PROCESS_AFTER_ORDER_CREATE');
$payment_modules->after_order_create($insert_id);
$zco_notifier->notify('NOTIFY_CHECKOUT_PROCESS_AFTER_PAYMENT_MODULES_AFTER_ORDER_CREATE');
// store the product info to the order
$order->create_add_products($insert_id);
$_SESSION['order_number_created'] = $insert_id;
$zco_notifier->notify('NOTIFY_CHECKOUT_PROCESS_AFTER_ORDER_CREATE_ADD_PRODUCTS');
//send email notifications
//-Uncomment the following line to enable the checkout-confirmation email to be sent
// $order->send_order_email($insert_id, 2);
$zco_notifier->notify('NOTIFY_CHECKOUT_PROCESS_AFTER_SEND_ORDER_EMAIL');