For most fills in graph builder, you can right click on the legend and select Transparency...
 
For example:
Open("$SAMPLE_DATA\Big Class.jmp");
Graph Builder(
    Variables( X( :height ) ),
    Elements( Histogram( X, Legend( 5 ) ) ),
    SendToReport(
        Dispatch(
            {},
            "400",
            ScaleBox,
            {Legend Model(
                5,
                Properties(
                    0,
                    {Fill Color( 5 ), Transparency( 0.5 )},
                    Item ID( "height", 1 )
                )
            )}
        )
    )
);