Jeśli dobrze zrozumiałem pytanie, da to pożądane rezultaty.
Query query = new Query(new Criteria().andOperator(
Criteria.where("name").is("name_1"),
Criteria.where("additionalData.additionalDataName").is("name_1_2")
));
query.fields().include("additionalData").exclude("_id");
List<Document> results = template.find(query, collectionName, org.bson.Document.class);