Shutdown times longer after update

Haven’t tried it myself but I think if I would want to achieve the unmounting just before shutdown I would try it with a systemd-service and this suggestion: https://unix.stackexchange.com/questions/39226/how-to-run-a-script-with-systemd-right-before-shutdown

In ExecStop=... you would put your umount command

If that HDD is wired to the SATA bus, and not an external USB disk, is it included in /etc/fstab so that it is automatically mounted/unmounted as a system disk?

Sata yes. I think it is included but i can give it a try and see if i can clean it up.

Easy to check, e.g.:

bruno@LT-B:~> lsblk
NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINTS
sda      8:0    0 232,9G  0 disk 
├─sda1   8:1    0   200M  0 part /boot/efi
├─sda2   8:2    0 175,8G  0 part /home
├─sda3   8:3    0    25G  0 part /
├─sda4   8:4    0     8G  0 part [SWAP]
└─sda5   8:5    0  15,9G  0 part /run/media/bruno/Leap16.0
sr0     11:0    1  1024M  0 rom  
bruno@LT-B:~>

Partitions or disks in fstab have a mountpoint defined in /etc/fstab but partitions or disks mounted by a user via gvfs (like my sda5 above) have a mount point like /run/media/<username>/<label>
and since your trouble points to gvfs I think that is the case for your problem disk too.

I found a way to unmount the disk when it was idling. That solved the problem entirely. Thanks, the problem was less complicated than thought, it was just a HDD thinking it was busy.

So for others looking here in the future, check in fstab and add argument of your choice https://wiki.archlinux.org/title/Fstab#Automatic_unmount.