@Entity annotated (mapping) classes are not at all related to the 'deprecated' entity beans from the J2EE architectural model. Not really anyway.
Those 'deprecated' entity beans you are reading about are very much still around, just that have been refactored so extensively as to be almost unrecognizable to someone used to old school J2EE.
In the new Java EE model, service and model classes are properly separated, with JPA annotated @Entity beans serving as the models, and @Stateless or @Stateful session beans serving as the service classes.
The key thing to keep in mind is separation of concerns.