apt-daily-upgrade.service looks like it could be your issue. This is an automatic unattended upgrade service that runs after
apt-daily.service. apt-daily runs the script /usr/lib/apt/apt.system.daily to download the updates, and apt-daily-upgrade runs the same script to do an unattended install of the updates.
You can see here that the apt-daily-upgrade.timer wont start until after apt-daily.timer has started. So you should be able to easily make these services start after boot by editing the apt-daily.timer service. Here is some more info from the man page about systemd timers if you want to check it out. This will explain my changes below.
In order to make this timer run the service 15 minutes after boot and only once a day (24hrs from last run unless you reboot again) after that, edit the [Timer] section of apt-daily.timer to look like this:
Here is the command to easily edit the timer using the default editor:
# systemctl edit apt-daily.timer
Here is a nice tutorial on how to use systemctl if you arent familiar:
NOTE: If you want to FULLY DISABLE the daily update/upgrade, run the following two commands (this is not recommended):
# systemctl disable apt-daily.timer
# systemctl disable apt-daily-upgrade.timer
Smartmontools is probably left in the image for USB HDD/SSDs and devices with EMMC storage. I would leave the package installed and just disable the service if it isn’t needed. This command will immediately stop smartmontools.service and prevent that service from starting on the next boot:
# systemctl disable smartmontools --now
update-notifier-download.service just tells you when updates are available. Shouldnt be causing any issues.
packagekit.service This is a small daemon that adds some functionality to APT. More info: PackageKit - What is PackageKit?
apport.service <- ?!? wut be this? Apport is an error reporting tool. It collects info about crashes and puts it in a standardized format for sending to bug trackers. You can disable this safely, but it isnt a bad thing to have running.