You know, it seems like a lot of these types of questions/issues could be easily defused by changing the names that calibre uses in the filesystem. That is, rather than storing folders by author name and books by title name, store them by some internal unique IDs. Thus a folder structure that currently looks like:
Could instead look like:
If you've ever tried to side-load books into Kindle on iPhone, for example, you'd see that while the app stores books in the filesystem it doesn't store them in any named manner that would make it easy for people to poke around.
There's no way to stop people from looking in places they shouldn't, but you can discourage it by making it difficult to figure out what everything is.