What would work out fairly well for this use case is to group files by similarity, and compress them with an algorithm which can look at all 'editions' of a text.
This should mean that storing a PDF with a (perhaps badly, perhaps brilliantly) type-edited version next to it would 'weigh' about as much as the original PDF plus a patch.
Depends. There are going to be some cases where files aren't literally duplicates, but the duplicates don't add any value -- for example, MOBI conversions of EPUB files, or multiple versions of an EPUB with different publisher-inserted content (like adding a preview of a sequel, or updating an author's bibliography).
Multiple versions of an EPUB with slightly different content is exactly the case where a compression algorithm with an attention span, and some metadata to work with can, get the multiple copies down enough in size that there's no point in disposing of the unique parts.
Also, some books included appendices, that are scanned in some versions but not in others, plus large posters, that are shrunk to a4 size in one version, split onto multiple a4 pages in another, and one huge page in a third version.
Then there are zips of books, containing 1 pdf + eg. example code, libraries, etc (eg progrmaming books).
I agree with samatman's position below: as long as the format is the slightest bit lossy -- and it always will be -- aggressive deduplication has more downsides than upsides.