Nieprawidłowo mapujesz pole identyfikatora zarówno na etapie projektu, jak i grupy.
Powinien to być _id nie id. Zmień także typ wiadomości e-mail na String. Działa dla mnie.
GroupOperation groupOp = Aggregation
.group("firstName", "lastName", "email", "status", "_id")
.addToSet("department").as("department").addToSet("address").as("address");
ProjectionOperation projectStage = Aggregation.project("firstName", "lastName", "email", "status", "department", "address", "_id");
...
AggregationResults<EmployeeOutFacet> EmployeeOutList = mongoTemplate.aggregate(aggregation, mongoTemplate.getCollectionName(Employee.class), EmployeeOutFacet.class);