Yes, customers can download the new version free of charge. However, there is no mechanism in the store to tell them that a new version is available.
You don't need a new ISBN for minor (and even fairly major) fixes. Whether to issue a new ISBN for a book update (such as a 2nd editition) is up to you. It is common to have even major fixes to books (such as for a 2nd "printing") without issuing a new ISBN.