I have installed Hortonworks hdp3.0 and configured Zeppelin as well.
When I am running spark or sql, Zeppelin is only showing me default database(This is the default database from Spark which has location as '/apps/spark/warehouse', not the default database of Hive). This is probably because hive.metastore.warehouse.dir property is not set from hive-site.xml and zeppelin is picking this from Spark config (spark.sql.warehouse.dir).
I had similar issue with spark as well and it was due to hive-site.xml file on spark-conf dir, I was able to resolve this by copying hive-site.xml from hive-conf dir to spark-conf dir.
I did the same for Zeppelin as well, copied hive-site.xml in zeppelin dir(where it has zeppelin-site.xml and also copied in zeppelin-external-dependency-conf dir.
But this did not resolve the issue.
After copying hive-site.xml from hive-conf dir to spark-conf dir, I restarted the spark services that reverted those changes, I copied hive-site.xml again and it's working now.
cp /etc/hive/conf/hive-site.xml /etc/spark2/conf