It depends how you use it. When you're still new to the data, using a freeflow text-and-codeblock workflow like jupyter or org-mode really speeds up the exploration phase.

Once you have a consistent set of questions, and methods to answer them, then yes, copy off the relevant chunks into their own scripts and source these when using similar data to bring you up to speed, and modify them to your tastes.

The issue with starting off with an external script initially is the distracting temptation to refine your code so it can be better used with future data, despite not yet having seen or not knowing what that future data is like. The initial "play and explore" phase of an analysis is very important imo, and notebooks really facilitate that.