A visual programming languages are often high level and can only take the user so far. If you were to make a programming editor mode that visually shows how programs are structured that understood standard programming languages it would be easier to understand the structure of these programs but the actual edits would likely still be done in the native language. Higher level edits might be very powerful but how often would you be able to do this safely? From a documentation point of view I agree with your assessment, the ability to understand how things work is easier visually at higher levels but we also have other tools to do this like UML. There are also editors like http://staruml.io/ that enable you to convert UML into code but I find this only works when projects are starting when you are trying to find the right high level abstractions. After this is set it is usually best to keep the high level structures that you have in place.
