You are correct normally barcode readers that are connected to the PLC through serial means (RS232, DeviceNet, Profibus) will transfer the data to the PLC in ASCII format. I am not sure what PLC you are using but it doesn't really matter. You will either have to do some math to convert the ASCII to decimal format or if the PLC language you use supports it, use a ASCII to Decimal(integer)function block and put the converted value in a PLC register. Next have your MES or SCADA interface reference to that register for the Barcode number.
What is MES? Manufacturing Execution System...the control layer above your SCADA (level II) system that interfaces with the business systems, usually for part tracking.
-Robert