Some said pdbedi is the replacement of smbpasswd and thus being replace. But it is not the case. smbpasswd do have some special user when using with LDAP backend. According to https://wiki.samba.org/index.php/Samba_%26_LDAP smbpasswd -w password is use to setup password bind to the ldap server and thus cannot be remove. it should be part of server.
Created attachment 364242 [details, diff] patch to make so that smbpasswd will be in both server and client flag.
+*samba-3.6.21 (30 Nov 2013) + + 30 Nov 2013; Lars Wendler <polynomial-c@gentoo.org> +samba-3.6.21.ebuild: + Version bump. Fixed installation of smbpasswd when "client" USE flag is unset + and "server" USE flag is set (bug #492888). +