This is the crux of it right here. You need to decide up front, thoughtfully and carefully - where you are going to put something. Just like in the physical world. Then you need to adjust and adapt it as you go. All the benefit comes downstream from those small additions to the workflow when you go to save something digitally.
And here I am, using Johnny Decimal for over five years and I can find everything all the time. As Johnny himself said below, if it doesn't work for you - that's cool - use something else. But you assertion that this can't work is not correct. It's just that it can't work for YOU.