Переименовать ограничение внешнего ключа в ManyToMany

Укажите inverseForeignKey:

@ManyToMany(fetch = FetchType.LAZY)                                                                         
@JoinTable(name = "clients__semantics_permissions",                                                         
           joinColumns = { @JoinColumn(name = "client_id", foreignKey = @ForeignKey(name = "client_fk")) }, 
           inverseForeignKey = @ForeignKey(name = "<the name you like>"))                                    
private Set<LevelTwoBase> semantics_level_two_base = new HashSet<LevelTwoBase>();                           

Hibernate-Output для создания схемы: (с использованием level_two_base_fk в качестве имени)

Hibernate: create table clients__semantics_permissions (client_id int8 not null, semantics_level_two_base_id int8 not null, primary key (client_id, semantics_level_two_base_id))
Hibernate: create table foo (id int8 not null, primary key (id))
Hibernate: create table level_two_base (id int8 not null, primary key (id))
Hibernate: alter table clients__semantics_permissions add constraint level_two_base_fk foreign key (semantics_level_two_base_id) references level_two_base
Hibernate: alter table clients__semantics_permissions add constraint client_fk foreign key (client_id) references foo