プロパティー

表示したいプロパティーには名前の頭に"_SubTex"とつけます．

    Properties
    {
        [PerRendererData] _MainTex ("Sprite Texture", 2D) = "white" {}
...
        // SubTexture
        [Toggle(USE_SUB_TEXTURE)] _UseSubTexture ("Use SubTexture", Float) = 0
        _SubTex("Sub Texture", 2D) = "white"{}
        [Header(Blend)]
        [KeywordEnum(Add, Mix)]
         _SubTexBlend("Blend", Float) = 0
         _SubTexBlendIntensity("Intensity", Range(0,1)) = 1
    }

Editor

using System.Collections;
using System.Collections.Generic;
using UnityEditor;

public class TSpritesEffectEditor : ShaderGUI {

	public override void OnGUI (MaterialEditor materialEditor, MaterialProperty[] properties)
	{
		var subTexToggle = ShaderGUI.FindProperty ("_UseSubTexture", properties);
		TShaderGUIUtils.DrawProperties (subTexToggle, "_SubTex", materialEditor, properties);
	}
}

ポイント

ShaderGUIを継承(MaterialEditorではない)
Toggleを取得
DrawPropertiesを呼ぶ

Util

using System.Collections;
using System.Collections.Generic;
using UnityEngine;
using UnityEditor;
using System.Linq;

public static class TShaderGUIUtils {
	/// <summary>
	/// Toggleで表示するUIを切り替える
	/// </summary>
	public static void DrawProperties(MaterialProperty toggle, string keyword, MaterialEditor materialEditor, MaterialProperty[] properties){
		
		materialEditor.ShaderProperty (toggle, toggle.displayName);

		if (toggle.floatValue == 1f) {
			var subTexProps = properties
				.Where (x => x.name.Contains (keyword))
				.Where (x => x.name != toggle.name);

			foreach (var prop in subTexProps) {
				materialEditor.ShaderProperty (prop, prop.displayName);
			}
		}
	}

}

プロパティーから対象のUIを検索して表示しています．

参考

MaterialEditorはOldみたいです．