Hi kmilo,
it depends on you application :-) Usually indexes are stored on filesystem (you might have configured it differently) so when your application restarts you don't need to reindex your database.
You mention session beans so I guess we're talking about EJBs?
If you know the database, schema, or application mapping changed after a redeploy then yes you should reindex the database; otherwise it's not needed.
In a similar situation I had created an MBean to reindex it all, so I could have the application server admin reindex the database as needed; a Session bean could do the same job, but there are situations in which you don't want to reindex it all: it might be a time-consuming task.
BTW there's a new reindexing routine in the latest beta:
http://in.relation.to/Bloggers/HibernateSearch32FastIndexRebuildbut yet again when you want to start it, that's up to your needs.