As you correctly noted, there is no JPA artifact that corresponds to the join table. Which means that you can execute such query only using a JDBC connection which has no affect on any internal state, PCtxt or 2-nd level cache (I don't think the spec supports executing an update or delete using native query, but even if it does, it doesn't parse such query to understand what it was doing).
[Message sent by forum member 'mvatkina' (mvatkina)]
http://forums.java.net/jive/thread.jspa?messageID=218232