Both H3 and H4 will default to use JTA tx managers and load datasources if configured so - i.e. JPA/EJB3 mode enables it by default.

In Seam 2 we generated a hibernate-console.properties file that sets a few properties to "convince" H3 to not load these things.

The important properties are:

hibernate.connection.provider_class=org.hibernate.connection.DriverManagerConnectionProvider
hibernate.datasource=
hibernate.transaction.manager_lookup_class=

Here are my recollection of the reasons:
hibernate.connection.provider_class needs to use DriverManager since otherwise it will load datasources.
hibernate.datasource needs to be overwritten/set to blank to ensure it will not lookup datasources
hiberante.transaction.manager_lookup_class needs to be overwritten/blank to ensure we don't get:

org.hibernate.HibernateException: The chosen transaction strategy requires access to the JTA TransactionManager
at org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:401)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1385)
at org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:954)
at org.hibernate.console.ConsoleConfiguration$4.execute(ConsoleConfiguration.java:268)
at org.hibernate.console.execution.DefaultExecutionContext.execute(DefaultExecutionContext.java:63)
at org.hibernate.console.ConsoleConfiguration.execute(ConsoleConfiguration.java:107)
at org.hibernate.console.ConsoleConfiguration.buildSessionFactory(ConsoleConfiguration.java:263)
at org.hibernate.eclipse.console.actions.ExecuteQueryAction.execute(ExecuteQueryAction.java:79)
at org.hibernate.eclipse.console.actions.ExecuteQueryAction.run(ExecuteQueryAction.java:55)
at org.eclipse.jface.action.Action.runWithEvent(Action.java:498)
at org.hibernate.eclipse.console.actions.ExecuteQueryAction.runWithEvent(ExecuteQueryAction.java:59)

Currently we probably just handle this when the settings are set to blank, but I think it starts to make sense to set these always.