Can I kill apt.system.daily to fix the apt install command?

Those are unattended upgrades, which acquire a different lock than the usual apt-get.

The simple way to install after the unattended upgrades pass is by waiting its lock to finish with flock. flock will wait until the lock is released and then it will execute sequentially update, upgrade and install.

 flock /var/lib/apt/daily_lock \
  apt-get -y update \
  && apt-get -y upgrade \
  && apt-get -y install \
    zip \
    unzip

References:

• Debian
• flock
• Another's man take

1: Check apt services installed with: systemctl list-units | grep apt

Disable the running apt services: systemctl disable apt*. e.g. sudo systemctl disable apt-daily.service

Refer a very clean process at: https://askubuntu.com/questions/1038923/do-i-really-need-apt-daily-service-and-apt-daily-upgrade-service

2: You might also want to set to zero or false some of the config values of apt.conf files at /etc/apt/apt.conf.d/10periodic

Refer: https://askubuntu.com/questions/1167314/disable-automatic-updates-ubuntu-18-04

You most likely will be good with #1 above.

Hope this helps

Thanks