Script to remove hidden/unused Layer Effects?

This can be due to layer protection. Try this variant.

var r = new ActionReference();      
r.putProperty(charIDToTypeID("Prpr"), stringIDToTypeID("targetLayers"));   
r.putEnumerated(charIDToTypeID("Dcmn"), charIDToTypeID("Ordn"), charIDToTypeID("Trgt"));  
  
if (executeActionGet(r).hasKey(stringIDToTypeID("targetLayers")))  
    {  
    var list = executeActionGet(r).getList(stringIDToTypeID("targetLayers"));  
  
    var offset = 0;  
    try { activeDocument.backgroundLayer } catch (e) { offset = 1; }  
    var unlock_flag = false;
    var lock = false;
    var del_cnt = 0;
  
    for (var n = 0; n < list.count; n++)  
        {  
        var idx = list.getReference(n).getIndex();  
  
        var r = new ActionReference();      
        r.putProperty(charIDToTypeID("Prpr"), stringIDToTypeID("layerEffects"));   
        r.putIndex(charIDToTypeID("Lyr "), idx+offset);  
  
        if (!executeActionGet(r).hasKey(stringIDToTypeID("layerEffects"))) continue;  
  
        var d = executeActionGet(r).getObjectValue(stringIDToTypeID("layerEffects"));  
        var r = new ActionReference();      
        r.putProperty(charIDToTypeID("Prpr"), stringIDToTypeID("layerLocking"));   
        r.putIndex(charIDToTypeID("Lyr "), idx+offset);  
        if (!unlock_flag) lock = executeActionGet(r).getObjectValue(stringIDToTypeID("layerLocking")).getBoolean(stringIDToTypeID("protectAll")); 
        for (var i = 0; i < d.count; i++)  
            {  
            var key = d.getKey(i);  
            var type = d.getType(key);  
      
            if (type == DescValueType.OBJECTTYPE)  
                {  
                var enabled = d.getObjectValue(key).getBoolean(stringIDToTypeID("enabled"));  
      
                if (!enabled)  
                    {  
                    if (lock && !unlock_flag)
                        {
                        var d2 = new ActionDescriptor();
                        var d1 = new ActionDescriptor();
                        var d3 = new ActionDescriptor();
                        var r = new ActionReference();
                        r.putIndex(charIDToTypeID("Lyr "), idx+offset);  
                        d1.putReference( charIDToTypeID( "null" ), r );
                        d3.putBoolean( stringIDToTypeID( "protectAll" ), false);
                        d2.putObject( stringIDToTypeID( "layerLocking" ), stringIDToTypeID( "layerLocking" ), d3 );
            
                        d1.putObject( charIDToTypeID( "T   " ), charIDToTypeID( "Lyr " ), d2 );
                        executeAction( charIDToTypeID( "setd" ), d1, DialogModes.NO );
                        unlock_flag = true;
                        }
                    var d2 = new ActionDescriptor();  
                    var r = new ActionReference();  
                    r.putClass(d.getClass(key));  
                    r.putIndex(charIDToTypeID("Lyr "), idx + offset);  
                    d2.putReference(stringIDToTypeID("null"), r);  
                    executeAction(stringIDToTypeID("disableSingleFX"), d2, DialogModes.NO);  
                    ++del_cnt;
                    }  
          
                }  
            }  
        }  
    alert(del_cnt + " LayerEffects have been removed");  
    }  
else  
    {  
    alert("no selected layers")  
    }