Will It Work If My Photos Are in Lots of Subfolders?
Yes. It walks the whole tree, however deep, and can flatten it into a date structure.
Yes. Point it at the top folder and it goes through everything underneath, however many levels deep, which is what a Takeout export needs since it nests by year and by album.
You can keep your existing folders or replace them with a date structure. Most people take the date structure, because it is the one that stays meaningful.
Takeout JSON Metadata Fixer previews the resulting folder tree before it moves anything. It runs on your own computer and is free for your first 500 photos.