Here’s some Jscript that shows how to find clusters hidden by ToggleVisibility.

Note that clusters can also be hidden by adding a visibility property (Property > Polygon Cluster Visibility).
Finding those would be a separate, but more straightforward, task

// Get a polygon cluster
//var oCluster = Dictionary.GetObject( "cube.polymsh.cls.Polygon" );
var oCluster = Selection(0);

// Get array of polygon indices
var a = oCluster.Elements.Array.toArray();

// Get [basically undocumented] invisible polygon cluster
var oGeometry = Dictionary.GetObject( "cube" ).ActivePrimitive.Geometry;
var l_polyVisCluster = oGeometry.Clusters( siInvisiblePolygonsClusterName );


// Check if a polygon in our cluster is hidden
// It is possible for a poly to be in multiple clusters
// Otherwise we could assume that if a[0] is hidden, 
// then the whole cluster is hidden

for ( var i = 0; i < a.length; i++ )
{

                if ( l_polyVisCluster.Elements.FindIndex( a[i] ) == -1 )
                {
                                LogMessage( "poly[" + a[i] + "] : Visible" );
                }
                else
                {
                                LogMessage( "poly[" + a[i] + "] : Hidden" );
                }
}

Here’s a snippet that shows how to loop through all material libraries and materials and delete unconnected shaders:

var oMatLibs = ActiveProject.ActiveScene.MaterialLibraries;
oEnum = new Enumerator( oMatLibs ) ;
for (;!oEnum.atEnd();oEnum.moveNext() )
{
	var oMatLib = oEnum.item() ;
	oEnum1 = new Enumerator( oMatLib.Items ) ;
	for (;!oEnum1.atEnd();oEnum1.moveNext() )
	{
		var oMat = oEnum1.item() ;
		DeleteUnusedShaders( oMat );
	}

}

The same thing but in Python.

oMatLibs = Application.ActiveProject.ActiveScene.MaterialLibraries
for lib in oMatLibs:
	for mat in lib.Items:
		Application.DeleteUnusedShaders( mat )

// Get all shaders
var x = FindObjects(null, "{6495C5C1-FD18-474E-9703-AEA66631F7A7}" );
LogMessage( x.Count );
var oShaderCollection = new ActiveXObject( "XSI.Collection" );

// Build up a collection of all Store in Channel shaders
oEnum = new Enumerator( x ) ;
for (;!oEnum.atEnd();oEnum.moveNext() )
{
	var oShader = oEnum.item() ;
	try {
		//LogMessage( oShader.ProgID );
		if ( oShader.ProgID.indexOf( "_storeinchannel" ) > 0 )
		{
			oShaderCollection.Add( oShader );
		}

	}
	catch(e)
	{
		LogMessage(e.message);
	}
}


LogMessage( oShaderCollection.Count );