While using Spring Data Rest after migrating an app to Spring Boot, I have observed that entity properties with @Id are no longer marshalled to JSON

By default Spring Data Rest does not spit out IDs. However you can selectively enable it through exposeIdsFor(..) method. You could do this in configuration, something like this

@Configuration
public static class RepositoryConfig extends
        RepositoryRestMvcConfiguration {

    @Override
    protected void configureRepositoryRestConfiguration(
            RepositoryRestConfiguration config) {
        config.exposeIdsFor(Class1.class, Class2.class);
    }
}