You did notice that these are in the "disabled by default" section of node_exporter, and you have to enable them with a CLI flag? (--collector.ntp)
# HELP node_ntp_leap NTPD leap second indicator, 2 bits.
# TYPE node_ntp_leap gauge
node_ntp_leap 0
# HELP node_ntp_offset_seconds ClockOffset between NTP and local clock.
# TYPE node_ntp_offset_seconds gauge
node_ntp_offset_seconds 1.4906e-05
# HELP node_ntp_reference_timestamp_seconds NTPD ReferenceTime, UNIX timestamp.
# TYPE node_ntp_reference_timestamp_seconds gauge
node_ntp_reference_timestamp_seconds 1.594660007565626e+09
# HELP node_ntp_root_delay_seconds NTPD RootDelay.
# TYPE node_ntp_root_delay_seconds gauge
node_ntp_root_delay_seconds 0.006286621
# HELP node_ntp_root_dispersion_seconds NTPD RootDispersion.
# TYPE node_ntp_root_dispersion_seconds gauge
node_ntp_root_dispersion_seconds 0.00541687
# HELP node_ntp_rtt_seconds RTT to NTPD.
# TYPE node_ntp_rtt_seconds gauge
node_ntp_rtt_seconds 0.0001571
# HELP node_ntp_sanity NTPD sanity according to RFC5905 heuristics and configured limits.
# TYPE node_ntp_sanity gauge
node_ntp_sanity 1
# HELP node_ntp_stratum NTPD stratum.
# TYPE node_ntp_stratum gauge
node_ntp_stratum 2