I use top-level notes primarily to summarize major topics. I group articles in folders, and then put a top-level note to summarize the main themes of the folder. So I would want to keep them in their folders.
Secondarily, I have been using them as a kludge to locate folders. Zotero (like Paperpile, I think) has no way of searching for folders, so when you get a complex folder structure you lose things. So I create a note in each folder with the title of the folder; I can search for the note, and then locate the folder it's in. It's clumsy, but it works. (I can also cross-reference those notes using the "Related" function, which is very useful.