This is a very real issue, and ignoring it doesn't make it go away.
I can show you the behavior for OpenLDAP (For ldap.stanford.edu, which has a root of "dc=stanford,dc=edu"
tribes:~> ldapsearch -x -h ldap -b "" | more
- extended LDIF
- base <> with scope subtree
- filter: (objectclass=*)
- requesting: ALL
o: Stanford University
l: Palo Alto
More importantly, is how are you going to handle people who have databases rooted at ""? That's what we do at Zimbra, as we support ISP's, and thus multiple domains that could exist across org, com, edu, etc. You should always be able to do a subtree search on "", and it should simply return the databases as they exist (according to ACL rules, etc, of course).
It is the same as any other subtree search.