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In terms of what you want to do for organizing your files, you could utilize Calibre to organize the naming. It may not be as simple as what you find in terms of music tagging and naming software, but I believe when you convert a file in Calibre, you can dictate its name. In other words, you might convert a mobi file to a mobi file to get the file name you want. It isn't as elegant as music files can be for just renaming, but it could work (I haven't tried it yet myself).
As for naming scheme. You really should choose what's right for you, but you probably already know that. By relying on programs like Calibre for my library (and other software for my music), I think of the file names as more of a backup to the most important info about the file, i.e. the bare minimum I would need to build a database again should I completely lose it. For a book, it seems like author and title would be a bare minimum. You've got that covered and then some. After that it just depends on what you have in your collection and how you look for files.
As an aside, I have a music library that exceeds 20,000 tracks now. However, I organize tracks differently because I tend to be an album oriented listener and it works best for me if each album is in its own subfolder. It doesn't mean it can't work in another configuration, but it is how I've done things. Books should be the same way.
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