My biggest (and only) issue with using tags instead of folders for hierarchical organization is that tags are not well supported on mobile (iOS), which I use heavily. In particular, the hierarchy is missing completely (it's flattened out).
Other than that, folders vs tags is more or less cosmetic, and I couldn't care less.
So, here's me, writing this comment, and hoping that someone from Evernote reads it and acts on it, however unlikely that may be.