The answer to your question will depend upon what you're trying to do. If you're looking for a LDAP server with a SQL server, then you should probably check out Oracle's OID system which is Oracle's LDAP server. Most directory servers don't use SQL because SQL is ineffecient for LDAP and unecessary. Most people believe you need an SQL server for transactions to keep things stable. But there are several flavors of embedded databases like Sleepycat's Berkeley Database (used by IPlanet among others) which provides for large databases that are extremely quick and still provide thing like transaction support (IPlanet uses this feature) so your directory server can recover its databases from a crash.
Next, SQL is a relational model, while JNDI supports a heiararchical model. Perhaps the better question is there an Object Database that supports JNDI? (And the answer is not that I know of, but they *could* exist)
If you're looking for a better object support for your Java applications from your databases, then you you should be looking into an object database or an API that allows object wrappers around JDBC ops.