My doctor's office doesn't toss loose documents into filing cabinets. Every document is in a folder. Perhaps you should use that example as a model. If you don't put any loose files in your documents folder, that should solve the problem for you.

Some tips, in no particular order…

You should also learn to leverage spotlight to quickly find the files and folders you want. I have many thousands of documents on my Mac, but I almost never browse through the documents folder looking for one.

Do you know that spotlight searches file contents, not just file names? Do you know about saved searches?

And don't forget that you can quickly jump to recent folders from the Finder's Go menu.

You may also find column view useful.