back in the 3x era when the modern file system was being developed folders initially got named monthly_MM_YYYY and in later versions it became more normalized to monthly_YYYY_MM which sorts better.  Any magic clean up tool that can go thru the uploads directory and refactor these folders to current standards, and potentially move orphaned files to a different directory?

There is no tool to do so, no, and it's actually not recommended. Doing so would break all external links to those files, including references throughout the suite itself.

but at one point the system had to upgrade and update all embedded referenced links in the body of posts, couldn't a clean up tool be built to do the same thing rename the directories then a search and replace for MM_YYYY to YYYY_MM? 

I still waiting for this feature to be returned...