Last week I installed Qubes 3.0 with Whonix templates. After I installed security updates, whonixcheck alerted me to the fact that unwanted packages had been pulled in by the updates, namely [tt]ntpdate[/tt] and [tt]chrony[/tt]. So I purged them as recommended by whonixcheck.
In order to avoid pulling in undesired packages, it might be wise to modify the apt configuration as recommended by Zwiebelfreunde for Tor Exit servers https://www.torservers.net/wiki/setup/server:
# disable debian default that pulls in recommended packages:
cat > /etc/apt/apt.conf.d/06norecommends <<EOS
APT
{
Install-Recommends "false";
Install-Suggests "false";
};
EOS