we created an app which writes its log into $SPLUNK_HOME/var/log/splunk
Event though the folder is being monitored with no blacklisted files, the application log is not being indexed. There is no mention to send_to_null_queue for this particular file so I am a bit confused.
This should work fine. I have my own log for my personal custom app and it writes to /opt/splunk/var/log/splunk/my_app.log and it is being read into _internal just fine - no additional inputs.conf stanzas required.