For AFP on anything but OS X, netatalk was missing a flush-to-disk command and failed the last time I surveyed.
Various samba versions have been implicated in backups that are corrupt when when you go to read them. There are enough people successfully using samba now for time capsule that I suspect that issue is a thing of the past or restricted to certain NAS devices.
Time Machine is a big enough bandwidth user that I presume we are talking LAN, and for many people their LAN is secure enough.
AFP and SMB are not encrypted AFAIK. Maybe you mean the authentication is not in clear text, but the data transfer is. (NFS doesn't really have authentication unless you use Kerberos, which doesn't pass cleartext credentials either.)
