Yes i use tags and it is great to search for notes but sometimes I don't have a clear idea what I am searching for and having some notes in particular folders makes me remember a piece of information I would have been forgotten. Tags is many times very useful but not always. Also seeing all notes inside a folder gives you a perfect view of the dimension of it.
Sometimes you forget to tag but having a piece of info inside a parent folder is an invaluable safe system so that the it does not get lost in chaos.....
if 2 levels have been possible don't see why 5,6 or 100 are not possible. It is really weird that they cannot give this demanded option to their users.
I love all the capture options of Evernote , the simplicity to use, to share, to tag ,etc but this limitations is really frustrating me on an on.....