While I have not installed it yet this was supposedly fixed in vCenter 4.1 Update 1 according to the Release Notes;
Messages for Datastore usage on disk or Datastore Disk Overallocation alarms display metrics in kilobytes instead of percent
The text in SNMP traps or email messages for Datastore usage on disk or Datastore Disk Overallocation alarms is inaccurate. The message displays the disk usage value in kilobytes when the value correlates to disk usage in percent.
This issue is resolved in this release.
Unfortunately, this still remains an issue;
The Datastore usage on disk alarm might not be triggered after vCenter Server is restarted *
The Datastore usage on disk alarm or an alarm that uses the Datastore Disk Usage (%) trigger type might not be triggered if vCenter Server is restarted.
Workaround: Edit the alarms making trivial changes such as changing the alarm description, everytime vCenter Server is restarted.