With direct mode, you're operating without large swathes of git-annex's carefully constructed safety net, which ensures that past versions of files are preserved and can be accessed. With direct mode, any file can be edited directly, or deleted at any time, and there's no guarantee that the old version is backed up somewhere else.
If you edit a file in Dropbox without it having had time to sync the previous version, what do you think it'll happen?
Git-annex with symlinks can add an extra layer of protection, in that you have to unlock the file before editing, so that it can ensure it has backed up. In direct mode, it just works like any other syncing systems - non-synced versions are lost.
That's without the Assistant, which further simplifies the latter steps by automatically taking care of committing and such. You just do unlock <file>, edit, then add <file>.
Yikes!