I wanted to check out the config file too… Didn't find ntopng.conf.
The package uses a different method to configure that service in pfSense.
Here is what I found:
there is 2 files related to ntopng in
/usr/local/pkg/ntopng.inc
/usr/local/pkg/ntopng.xml
This file :/usr/local/pkg/ntopng.inc seems to have all the logic for configurations included.
and seems to start ntopng on the fly with config parameters based on the the xml config file / web page
It starts something like this
(after looking at ps -A)
/usr/local/bin/ntopng -d /var/db/ntopng -G /var/run/ntopng.pid -s -e -w 0 -W 3000 -i em1 --dns-mode 0 --local-networks 192.168.0.0/16,172.16.0.0/12,10.0.0.0/8
Perhaps that info helps you further...