Disabling or overriding the udisks probe for ATA SMART support udev rule will prevent Gnome Disk Utility 3.0.2 (Ubuntu 12.04 in my case) from showing the hard disk failing notification. From the comments at https://bugs.launchpad.net/ubuntu/+source/linux/+bug/574462/comments/7 this workaround acceptable.
Create a file with the following contents at /etc/udev/rules.d/81-udisks-no-ata-smart.rules so that it overrides /lib/udev/rules.d/80-udisks.rules.
# Force all disk probes to return not ATA SMART capable so that a drive with SMART
# failures does not trigger Gnome Disk Utility to display a pop-up warning message.
# Note: Some programs that rely on udisks to perform SMART checks may not work.
# However, manual SMART reads (e.g. using smartctl) are not be affected.
# USB ATA enclosures with a SAT layer
KERNEL=="sd*[!0-9]", ATTR{removable}=="0", ENV{ID_BUS}=="usb", ENV{DEVTYPE}=="disk", ENV{UDISKS_ATA_SMART_IS_AVAILABLE}="0"
# ATA disks driven by libata
KERNEL=="sd*[!0-9]", ATTR{removable}=="0", ENV{ID_BUS}=="ata", ENV{DEVTYPE}=="disk", ENV{UDISKS_ATA_SMART_IS_AVAILABLE}="0"
# ATA disks connected via SAS (not driven by libata)
KERNEL=="sd*[!0-9]", ATTR{removable}=="0", ENV{ID_BUS}=="scsi", ENV{DEVTYPE}=="disk", ENV{ID_VENDOR}=="ATA", ENV{UDISKS_ATA_SMART_IS_AVAILABLE}="0"