The purpose of Lightbox isn’t to be easier necessarily. There may always be an extra click or two involved when opening subfolders. It’s purpose is to be a tidy, well organized hub for on-demand content that won’t be required in every single session, otherwise free of much impact on the program, and easily portable between program versions.
I agree with you that two additional items would probably not be much of an issue other than adding clutter to the Tool menu–if you stopped there. But newer users can be overly aggressive in adding all sorts of items to the startup, and in my experience, this will increase your chances of ending up back here with some sort of unexplained issue. When troubleshooting problems one has to subtract variables, and a heavily modified Zbrush startup adds a lot of variables.
It is my recommendation that you use Lightbox whenever possible rather than add many items (materials, brushes, whatever) directly to the startup. In the long run, it may be easier than dealing with the potential issues associated with not doing this.