If I had to guess, it's because the FreeBSD port of ntopng is likely the open source/community version, which probably doesn't have a way to support a commercial license. You'd need to get the ntop folks to create a pfSense package for their commercial version that could be installed in order to use a paid license.
Of course, they'd say "Why are you running this on a router/firewall?", and they'd probably try to direct you to their ARM versions, even though pfSense runs on Intel/AMD CPUs (with the exception of the newer Netgate produced devices; SG-1000 and SG-3100 are both ARM devices).