no elasticsearch does not join documents, but you can issue your sql statement to pull all the joins of all users. if I get you right you want all this users data in Elasticsearch.
from the little that I know about what your doing,
is that you have a Mysql Database with all your user data, and you want to load that data in to elasticsearch. Which is totally possible,
However Logstash is only a simple reader of data with some data manipulations capacity, doing complex data or dynamic data is not really its strong suite. As an example but there are plenty of other answers to accomplish this
you could write a php command (or lang of choice) to query and write the data to a file in say JSON , then either have that same PHP insert it to Elastic search or have Logstash do it.
Heck you probably could set up a DB Trigger to post the data directly to Logstash via HTTP every-time the user updates his data (a quick example) don't know if it is good for you.