Currently, nothing stops a user from setting up ~/annex, adding some special remote, and never once ending up with a clone of their repository, so there is really no backup of the repository as a whole, despite the special remotes.
Potentially adding to the confusion, they might have remotes in repository groups "full backup" or "backup", and so think everything is backed up.
Webapp could count the number of known remote uuids that are not special remotes, and require there to be at least numcopies of them (excluding the current repo I suppose), and pop up a nudge with a button that presents the various available ways to make a non-special remote.
Working out if a remote uuid is a special remote is probably the hard bit. A special remote will be listed in uuid.log, with a type other than gcrypt or git. Any other uuid, that is not dead, can count as 1 clone. This does not handle git remotes that are not using git-annex (eg github), so it could also look through the git remote list and count any that don't have an annex-uuid.