If id, type and destination index of the documents are the same, by default it should not create another instance of the same document, but rather just bump the version number of the already indexed document.
You can always try changing the default action of the output plugin to create instead of the default index (as per https://www.elastic.co/guide/en/logstash/1.5/plugins-outputs-elasticsearch.html#plugins-outputs-elasticsearch-action), so the insert will fail for already existing documents.
Keep in mind though that you will potentially be flooded with 40x error responces from ES. Nothing to worry about since it's intended, but may take up space quickly depending on the amount of them.