The standard Magento API has an inherent flaw where the Shipment Email that is sent to customers when a shipment is created does NOT contain the associated tracking number. This is a result of the "Add Tracking" API call being separate from the "Shipment Create" API. By default the "Shipment Create" API triggers the shipment email, before the "Add Tracking" API has had a chance to assign the tracking number to the shipment.
The extension that is attached to this KB article can be installed by your Magento Developer to Enhance the Magento Shipment API Process. It makes the following 2 changes to the standard Magento API process.
(1) The shipment email that is normally sent during the "Shipment Create" API call is supressed
(2) The shipment email is sent AFTER the "Add Tracking" API call is made
Note: This shipment email with tracking number is ONLY sent if shipment emails are enabled in the Magento Admin