Yes, I think the need for an additional field for an internal ID is easy to see and something like this will be added for sure. Books that don't have an ISBN could use the ISBN field or separate field for ID. You can also decide to just leave the ISBN field empty and fill in only the book titles if that works for you. Books with different covers could simply have the same ISBN and different cover images, so no problem there either as far as I can see.
ISBN number validation will surely be implemented.
Bookmarks