The problem is that you are copying the .indb. This is really nothing more than a collection of pointers to the documents, and unless you explicitly replace the documents in the book panel each day, your pointers don't change and they still refer to the original files.
The easiest thing is probably to simple create a new .indb file each day and add the copied files to it.
Normally for these tasks special redaction and content management tools are used, as versioning is used often only with stories and not whole document.
I would recommend to leave the book file as it is. But when you start to make change, than save as copy with the date, like file_2014-06-18.indd I recommend also to use the ISO style of date, this will keep the files in alphabetical order according their age. The original file remains part of the book as actual file, the copy is for documentation only.
if your file structure looks a bit like this:
I’d do something like Willi suggested: Just zip the whole folder [MyBook1], add the date and do it aside for documentation.