Consider that "cleaning and organizing" your code means that it is no longer the code that actually produced the results in your paper! The fact that your code

Consider that "cleaning and organizing" your code means that it is no longer the code that actually produced the results in your paper! The fact that your code is a mess means that it might be buggy; if other people can see your code, someone might find a bug in it. As you said, this is a good thing for open science, and makes your work easier to reproduce.