Only certain method hit the cache. From the documentation:
Whenever you pass an object to save(), update() or saveOrUpdate() and whenever you retrieve an object using load(), get(), list(), iterate() or scroll(), that object is added to the internal cache of the Session.
Anytime you run a query whether from Criteria, HQL, or SQL Hibernate will NOT get data from the second level cache.
But if you turn on the second level query cache, then some queries can go to the query cache. In the query cache only IDs are stored. And there is a requirement that the Objects those IDs represent must be in the standard second level cache in a cache region.
One issue you have with the query cache is that the resultset could get stale real quickly if data is inserted or deleted from the database.