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.

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.