How to have custom script icons other than using "Assets/Gizmos" in Unity3D

You can set the icon with figure 5 and then turn the gizmos for that icon off from the gizmos drop down.

Edit: Injunction with the step above you could try this script derived from here it uses reflection to find the class responsible for turning off the the gizmos and icons. This would execute any time your scripts recompiled to keep those icons off or if you added any new icons to the autohide icon file. Note: scriptClass will be an empty string for built in components eg.Camera, AudoSource

using UnityEditor;
using System;
using System.Reflection;

public class DisableAllGizmos
{
    [UnityEditor.Callbacks.DidReloadScripts]
    private static void OnScriptsReloaded()
    {
        var Annotation = Type.GetType("UnityEditor.Annotation, UnityEditor");
        var ClassId = Annotation.GetField("classID");
        var ScriptClass = Annotation.GetField("scriptClass");
        var Flags = Annotation.GetField("flags");
        var IconEnabled = Annotation.GetField("iconEnabled");

        Type AnnotationUtility = Type.GetType("UnityEditor.AnnotationUtility, UnityEditor");
        var GetAnnotations = AnnotationUtility.GetMethod("GetAnnotations", BindingFlags.NonPublic | BindingFlags.Public | BindingFlags.Static);
        var SetIconEnabled = AnnotationUtility.GetMethod("SetIconEnabled", BindingFlags.NonPublic | BindingFlags.Public | BindingFlags.Static);

        Array annotations = (Array)GetAnnotations.Invoke(null, null);
        foreach (var a in annotations)
        {
            int classId = (int)ClassId.GetValue(a);
            string scriptClass = (string)ScriptClass.GetValue(a);
            int flags = (int)Flags.GetValue(a);
            int iconEnabled = (int)IconEnabled.GetValue(a);

            // this is done to ignore any built in types
            if (string.IsNullOrEmpty(scriptClass))
            {
                continue;
            }

            // load a json or text file with class names

            const int HasIcon = 1;
            bool hasIconFlag = (flags & HasIcon) == HasIcon;

            // Added for refrence
            //const int HasGizmo = 2;
            //bool hasGizmoFlag = (flags & HasGizmo) == HasGizmo;

            if (/*Compare class names in file to scriptClass == true*/)
            {
                if (hasIconFlag && (iconEnabled != 0))
                {
                    UnityEngine.Debug.LogWarning(string.Format("Script:'{0}' is not ment to show its icon in the scene view and will auto hide now. " +
                        "Icon auto hide is checked on script recompile, if you'd like to change this please remove it from the config",scriptClass));
                    SetIconEnabled.Invoke(null, new object[] { classId, scriptClass, 0 });
                }
            }
        }
    }
}

1. Shown in the inspector with a gizmo

   

2. Hide Icon from gizmos dropdown

   

3. Icon still appears in the inspector and in the project view but not in the scene