If an index exists but is empty, it seems that Logstash throws an exception when searching via Kibana.
Delete a type from an index. In my tests, it was the only type in the index, leaving it empty after deletion:
Using Kibana, any queries including 2012/12/30 throws the exception attached.
Deleting the index entirely works okay.
This is not related to logstash, but to how Kibana query Elasticsearch and the explanation is in the stacktrace
Cannot try to sort on a missing field (as there is no data)...
It would be better for you to report your case on kibana project issues
maybe the author have plan for this "corner" case already.