Yes they will fit. Up until the 2010 model year the GT500 didn't get a model specific muffler. It used the stock GT muffler for the automatic. People get pulled in by the "Shelby GT500" connection and pay for parts that are just off the shelf stuff. (like the side skirts - the GT500 just used the same textured black skirts as the 2005-09 V6, but people paid big dollars for them because of the connection)
So if you are buying them, price them the same as any GT muffler.