I'd suspect https://bugs.launchpad.net/network-manager/+bug/211631 first myself.
Although those mounts are meant to be brought up/down by KDE, if Samba or NetworkManager was screwed by the upgrade at the time, this might have failed.
$ cat ~/.kde/Autostart/mountcifs.sh 
#!/bin/bash
sleep 30
sudo mount /home/falken/smb4k/bookcase-falken
...

$ cat ~/.kde/shutdown/umountcifs.sh 
#!/bin/bash
sudo umount -t cifs -a

No, I don't get unclean shutdown messages, and shutdown is normally very quick. It took ages after the upgrade, but is now quick again.

debsums produces no output.

falken@wopr:/tmp$ ls -l /etc/init.d/umountroot*
-rwxr-xr-x 1 root root 2926 2011-07-14 06:11 /etc/init.d/umountroot
falken@wopr:/tmp$ 

falken@wopr:/tmp$ ls -l /etc/rc6.d/
total 4
lrwxrwxrwx 1 root root  17 2010-09-26 10:08 K01apache2 -> ../init.d/apache2
lrwxrwxrwx 1 root root  16 2009-11-23 21:38 K01dhcdbd -> ../init.d/dhcdbd
lrwxrwxrwx 1 root root  15 2010-09-26 10:08 K01exim4 -> ../init.d/exim4
lrwxrwxrwx 1 root root  13 2008-05-18 17:19 K01gdm -> ../init.d/gdm
lrwxrwxrwx 1 root root  20 2009-11-23 21:38 K01kerneloops -> ../init.d/kerneloops
lrwxrwxrwx 1 root root  16 2009-11-23 21:38 K01lindvd -> ../init.d/lindvd
lrwxrwxrwx 1 root root  19 2009-11-23 21:38 K01mysql-ndb -> ../init.d/mysql-ndb
lrwxrwxrwx 1 root root  17 2010-09-26 10:17 K01openvpn -> ../init.d/openvpn
lrwxrwxrwx 1 root root  19 2010-01-29 19:34 K01setserial -> ../init.d/setserial
lrwxrwxrwx 1 root root  18 2010-11-05 21:33 K01timidity -> ../init.d/timidity
lrwxrwxrwx 1 root root  17 2010-09-26 10:17 K01vboxdrv -> ../init.d/vboxdrv
lrwxrwxrwx 1 root root  23 2010-01-29 19:34 K02etc-setserial -> ../init.d/etc-setserial
lrwxrwxrwx 1 root root  23 2009-11-23 21:38 K02mysql-ndb-mgm -> ../init.d/mysql-ndb-mgm
lrwxrwxrwx 1 root root  22 2009-11-23 21:38 K02spamassassin -> ../init.d/spamassassin
lrwxrwxrwx 1 root root  20 2010-09-26 10:17 K06umountcifs -> ../init.d/umountcifs
lrwxrwxrwx 1 root root  22 2010-09-26 10:08 K08umountnfs.sh -> ../init.d/umountnfs.sh
lrwxrwxrwx 1 root root  33 2011-04-22 11:08 K20vboxballoonctrl-service -> ../init.d/vboxballoonctrl-service                                                                                         
lrwxrwxrwx 1 root root  25 2010-10-11 18:52 K20vboxweb-service -> ../init.d/vboxweb-service
lrwxrwxrwx 1 root root  17 2009-10-04 08:38 K25hwclock.sh -> ../init.d/hwclock
lrwxrwxrwx 1 root root  19 2010-11-05 21:30 K74bluetooth -> ../init.d/bluetooth
lrwxrwxrwx 1 root root  21 2011-04-18 19:19 K99laptop-mode -> ../init.d/laptop-mode
-rw-r--r-- 1 root root 351 2011-07-14 06:11 README
lrwxrwxrwx 1 root root  16 2009-11-23 21:38 S01reboot -> ../init.d/reboot
lrwxrwxrwx 1 root root  18 2009-11-23 21:38 S01sendsigs -> ../init.d/sendsigs
lrwxrwxrwx 1 root root  18 2009-11-23 21:38 S01umountfs -> ../init.d/umountfs
lrwxrwxrwx 1 root root  20 2009-11-23 21:38 S01umountroot -> ../init.d/umountroot
lrwxrwxrwx 1 root root  17 2010-09-26 10:08 S02urandom -> ../init.d/urandom
lrwxrwxrwx 1 root root  29 2011-04-05 21:55 S10unattended-upgrades -> ../init.d/unattended-upgrades                                                                                                 
lrwxrwxrwx 1 root root  20 2011-09-23 21:44 S35networking -> ../init.d/networking
lrwxrwxrwx 1 root root  20 2011-04-05 21:59 S48cryptdisks -> ../init.d/cryptdisks
lrwxrwxrwx 1 root root  26 2011-04-05 21:59 S59cryptdisks-early -> ../init.d/cryptdisks-early
falken@wopr:/tmp$ 

While I understand the need to be cautious, my experience was almost as bad as it could get (I had no network (wireless, but if NetworkManager is dead would even system wired ones work ?), and no X. As you say, if this was a remote system, or one owned by a normal user, it'd be a tough one to fix.