Writing a bunch of scripts can quickly become a mess. I was working on some twitter analysis for a project, and not really worrying about the code because I didn't intend for it to be used again, and it quickly became a mess of "run this script, then run that script on the generated file, then use this shell command to process the file, then run the final analysis step on that file, then clean up all the intermediates". Not to mention, say, "one-time" data cleanup through the shell / REPL that runs into problems months down the line when you want to update the data set. And, of course, invariably none of this is documented. Notebooks don't force you to organize your code and write documentation, but they strongly encourage it.