For awhile I tried keeping all my weekly columns in a giant scrivener file, then one file per year of columns, then finally decided on one file per project. I normally toss the scrivener project file after exporting the completed draft to rtf. All the research files exist in rtf or txt files that I then import into the project they’re needed in, so if I need to keep any of those, I still have them.
For my book in progress, it’s one project per section, each one being around 30000 words, subdivided into lots of chapters.
The reasons I went to one project for file are those stated in others’ comments above. What with spotlight and Finder folders, I found I didn’t need a second repository for files once the story was drafted, although it wouldn’t surprise me if other writers needed scrivener’s references, keywords or other features not available or as convenient in the Finder.