>> Socket.gethostname
=> "prod1"

>> Socket.gethostbyname(Socket.gethostname).first
=> "prod1.mydomain.com"

$ hostname
prod1

$ hostname -f
prod1.mydomain.com

from the 'hostname' man page:
 -f, --fqdn, --long
              Display  the FQDN (Fully Qualified Domain Name). A FQDN consists
              of a short host name and the DNS domain  name.  

This probably could be changed in the configuration, but I'm not entirely convinced it should be. 

There's also a discussion about this on Stackoverflow:
http://serverfault.com/questions/331936/setting-the-hostname-fqdn-or-short-name

It seems to me it would be best to be able to set this as a logstash configuration option so people don't have to make changes in pre-existing environments that could possibly have unintended consequences.