According to the http://docs.geotools.org/latest/userguide/library/jdbc/datastore.html - docs I used the code below to get an H2Datastore configured by JNDI:
JDBCDataStore datastore = (JDBCDataStore) DataStoreFinder.getDataStore(params);
While retrieving the functional factories by dbtype H2DataStoreFactory and H2JNDIDataStoreFactory were returned. This is correct but in the next step the usability of each gets checked. At first H2DataStoreFactory is checked and also selected because it needs only the type (user and so on are optional). So it is used to generate the store without checking H2JNDIDataStoreFactory which fits definitely better because jndiReferenceName (JDBCJNDIDataStoreFactory.JNDI_REFNAME.key) is defined.
In last consequence an file database null.*.db is created in the execution folder. I recognized this behavior also in the http://sourceforge.net/projects/geotools/files/GeoTools%208.0%20Releases/8.0-RC1/ - gt-project download where I found null-database in the zip (see attachment).