ntpdate doesn't parse the /etc/ntp.conf file. The program
ntpdate-debian is provided that reads its server list from
/etc/default/ntpdate or alternatively from /etc/ntp.conf.

ntpdate is run whenever a network interface is brought up. To adjust
this behavior, the file /etc/network/if-up.d/ntpdate should be edited.

Note that ntpdate is *not* really intended to be used by hosts with
good network connectivity. The "ntp" 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. If all you want is to set the clock
to a reasonable value once in a while, a more light-weight package
like "rdate" can also do the job.