ntpdate doesn't parse the ntp.conf file. The program ntpdate-debian is provided that reads its server list from /etc/default/ntpsec-ntpdate or alternatively from /etc/ntpsec/ntp.conf. ntpdate is run whenever a network interface is brought up. To adjust this behavior, the file /etc/network/if-up.d/ntpsec-ntpdate should be edited. Note that ntpdate is *not* really intended to be used by hosts with good network connectivity. The "ntpsec" package, which provides a persistent daemon that does a better job of keeping system time than even a cron'ed invocation of ntpdate, is a better choice for systems with good network connectivity.