When you set some right click options, like removing desktop icon or disable the products own self update) on the All Products folder in the hierachy, those settings should be applied to both existing and later on added products. Today the setting will only be applied to existing products, so If you add new products, you need to remember to check if the application supports it and then modify the right click options for the newly added products. Things set on the All Products folder should be inherited and applied to all objects in the folder tree.
This should behave better now. Let us know if you still experience issues with right click options set at the vendor, or all vendor level.