It seems that it is not possible to clear up an previously populated eZISBN datatype on a class. If the attribute is set to be optional, eZ Publish correctly accepts empty field (which was previously filled in with valid ISBN number), but stores the previous value, not the empty one.
I used this
as a temporary fix (not sure if it is correct, but for my case it does the job).
On some class with ISBN datatype (ISBN13 type, not-required) add valid ISBN number. Store and edit again, try to remove the value by removing the previously entered value from the field. Store again - the original value shows up in the object, should be empty.