Did you manually copy the geo files to the appropriate folder? I've had to do this for each upgrade of OPNsense (a couple exceptions maybe...but mostly every time). I'm not running ntopng since 12.1.5 as it causes excessive CPU usage for me...but this is the procedure I would need to perform to get the geo data feature enabled (along with the google api key for the map).
Copy files to /usr/local/share/ntopng/httpdocs/geoip/ (from MaxMind)
GeoLite2-ASN.mmdb
GeoLite2-Country.mmdb
GeoLite2-City.mmdb
chmod +x /usr/local/opnsense/scripts/OPNsense/Ntopng/generate_certs.php
Copy files to /usr/local/share/ntopng/httpdocs/geoip/ (from MaxMind)
GeoLite2-ASN.mmdb
GeoLite2-Country.mmdb
GeoLite2-City.mmdb
chmod +x /usr/local/opnsense/scripts/OPNsense/Ntopng/generate_certs.php
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