Performance of elastic queries
The top-level filter element in the first request has very special function in Elasticsearch. It's used to filter search result without affecting facets. In order to avoid interfering with facets, this filter is applied during collection of results and not during searching, which causes its slow performance. Using top-level filter without facets makes very little sense because filtered and constant_score queries typically provide much better performance. If verbosity of filtered query with match_all bothers you, you can rewrite your second request into equivalent constant_score query:
{ "query": { "constant_score": { "filter": { "term": { "id": "123456" } } } }}