I've tried adding the following to my script but it appears to have no effect at all in CS5 on Windows 7.
app.userInteractionLevel = UserInteractionLevel.DONTDISPLAYALERTS;
Does this still work for anyone else?
The following example displays the alert when I execute it.
#target Illustrator
app.userInteractionLevel = UserInteractionLevel.DONTDISPLAYALERTS;
alert('Hi there!');
app.userInteractionLevel = UserInteractionLevel.DISPLAYALERTS;