Well, apparently was easier than I thought.
Example using InheritanceStrategy.JOINED
First Step
generate your three classes Employee and it's subclasses RegularEmployee and ContractEmployee as if they were separate classes, except for the fact that you won't be repeating the inherited attributes on the subclasses.
Second Step
Add the annotations on the Employee class to tell hibernate that it's going to be the super class you can find how to do that here
REMOVE the id generation type annotations because your subclasses instances to have the same ID as their parent instance.
@Id // this should be gone
@GeneratedValue(strategy = GenerationType.AUTO) // this should be gone
@Column(name="id")// this should be gone
private Long id;// this should be gone
Third Step
add the extends Employee to the java subclasses.
Fourth Step
here you should be able to use $scope inheritance on angular, but I'm new to it, so I don't know how to do it on the app structure that jhipster uses I'll be grateful if someone tells me how to improve this
on your contractEmployee-dialog.html and regularEmployee-dialog.html add the inherited fields from Employee, so that you can generate a Model that can be saved properly by hibernate, otherwise you will get validation errors.
Fifth Step
Build and test.