JNDI is really a standard API for "directory lookup" service to managed objects. Generally we put different type of objects in JNDI (even X509 certs). Queue/Topics are usually put there by MOM providers, so that we can all get to them via standard JNDI API.
JNDI is used to standardis access to LDAP for example where you can lookup DN entries etc. similar to how JDBC API is used for accessing various DBMS vendors, or JMS for accessing various MOM providers.