Well, I somehow resolved it...
Sort of, I downloaded the configuration manually edited the XML file, removing the <ntpd>...</ntpd> section. Did a restore of full configuration, after the reboot it works, checked the NTP configuration, all looks the same. Even Debug output is all the same except now both IPv4 127.0.0.1 and IPv6 ::1 query through ntpq work.
Only thing I can figure is that there is a hidden or corrupted character in old ntp configuration section.