I can indeed trigger it in cosmic with an upgrade from 1:2.12+dfsg-3ubuntu8 -> 1:2.12+dfsg-3ubuntu8.6

But forcing the same (by enabling cosmics sources) in Disco does not trigger the bug (1.10ubuntu5).
You will need an equiv trick to verify Disco as well I think.

Here he logs of the cosmic verify:

# trigger bug before upgrade
/etc/qemu/fsfreeze-hook
found conffile /etc/qemu/fsfreeze-hook in new pkg but on dpkg status
An error occurred: [Errno 21] Is a directory: '/etc/qemu/fsfreeze-hook'
Traceback (most recent call last):
  File "/usr/bin/unattended-upgrade", line 1669, in main
    install_start_time)
  File "/usr/bin/unattended-upgrade", line 1875, in run
    if conffile_prompt(item.destfile):
  File "/usr/bin/unattended-upgrade", line 1015, in conffile_prompt
    with open(prefix + conf_file, 'rb') as fp:
IsADirectoryError: [Errno 21] Is a directory: '/etc/qemu/fsfreeze-hook'
Extracting content from /var/log/unattended-upgrades/unattended-upgrades-dpkg.log since 2019-05-03 05:45:41
Traceback (most recent call last):
  File "/usr/bin/unattended-upgrade", line 2138, in <module>
    sys.exit(main(options))
  File "/usr/bin/unattended-upgrade", line 1669, in main
    install_start_time)
  File "/usr/bin/unattended-upgrade", line 1875, in run
    if conffile_prompt(item.destfile):
  File "/usr/bin/unattended-upgrade", line 1015, in conffile_prompt
    with open(prefix + conf_file, 'rb') as fp:
IsADirectoryError: [Errno 21] Is a directory: '/etc/qemu/fsfreeze-hook'

# upgrade to proposed
apt install unattended-upgrades
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Suggested packages:
  bsd-mailx default-mta | mail-transport-agent needrestart
The following packages will be upgraded:
  unattended-upgrades
1 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Need to get 41.8 kB of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu cosmic-proposed/main amd64 unattended-upgrades all 1.5ubuntu3.18.10.4 [41.8 kB]
Fetched 41.8 kB in 0s (535 kB/s)            
Preconfiguring packages ...
(Reading database ... 46512 files and directories currently installed.)
Preparing to unpack .../unattended-upgrades_1.5ubuntu3.18.10.4_all.deb ...
Unpacking unattended-upgrades (1.5ubuntu3.18.10.4) over (1.5ubuntu3.18.10.3) ...
Processing triggers for systemd (239-7ubuntu10.13) ...
Setting up unattended-upgrades (1.5ubuntu3.18.10.4) ...
Processing triggers for man-db (2.8.4-2) ...


# retry with fix
root@c:~# sudo unattended-upgrade -d
Initial blacklisted packages: 
Initial whitelisted packages: 
Starting unattended upgrades script
[...]
check_conffile_prompt(/var/cache/apt/archives/qemu-guest-agent_1%3a2.12+dfsg-3ubuntu8.6_amd64.deb)
found pkg: qemu-guest-agent
conffile line: /etc/init.d/qemu-guest-agent f61a64ac1e48993023018fd1cff85191
current md5: f61a64ac1e48993023018fd1cff85191
conffile line: /etc/qemu/fsfreeze-hook/fsfreeze-hook 15f6ff42cbc5550a07ee21c2a471d905
current md5: 15f6ff42cbc5550a07ee21c2a471d905
blacklist: []
whitelist: []
Packages that will be upgraded: qemu-guest-agent
Writing dpkg log to /var/log/unattended-upgrades/unattended-upgrades-dpkg.log
applying set ['qemu-guest-agent']
(Reading database ... 46512 files and directories currently installed.)
Preparing to unpack .../qemu-guest-agent_1%3a2.12+dfsg-3ubuntu8.6_amd64.deb ...
Unpacking qemu-guest-agent (1:2.12+dfsg-3ubuntu8.6) over (1:2.12+dfsg-3ubuntu8) ...
Setting up qemu-guest-agent (1:2.12+dfsg-3ubuntu8.6) ...
Processing triggers for systemd (239-7ubuntu10.13) ...
Processing triggers for man-db (2.8.4-2) ...
left to upgrade set()
All upgrades installed
InstCount=0 DelCount=0 BrokenCount=0
Extracting content from /var/log/unattended-upgrades/unattended-upgrades-dpkg.log since 2019-05-03 05:49:31

Mark cosmic as verified