As you can see here, the values are passed to pleaserun. But you have also noticed that the values do not appear in /etc/systemd/system/logstash.service. This is because systemd unit files do not assign nice values or allow establishment of file handle limits. File handles and nice values (per user) should be handled in /etc/security/limits.conf for the Logstash user:
logstash - nofile 262143
logstash - nice 19
The same approach should be used in all startup forms, actually: init, upstart, and systemd. For upstart, uncommenting the appropriate lines in /etc/init/logstash may yield the desired result, but are still not preferred over settings in /etc/security/limits.conf. Editing of this file by Logstash at install time is not going to be well received by security professionals, so we leave it to the end user.
Putting custom services directly in this directory is the only way to guarantee that the service is recognized across platforms (RPM platforms, DEB platforms, etc). This is actually done by pleaserun, because it's the only commonly searched path across all known distributions using systemd. It took us a considerable amount of digging to find and verify this.