In CS3, the following code would open any InDesign doc with no UI. Missing links and missing fonts dialogs were suppresed:
var myFile = new File("some location");
var showWindows = false;
var myDoc = app.open(myFile,showWindows);
In CS4, there's a new missing links alert. It's different from the CS3 alert - it just tells you how many links aren't connected to sources, and lets you click OK. It now shows up if you open a doc with missing links, even if you set showWindows to false.
You can disable it by going under Preferences > File Handling and turning off "Check links before opening document", but it would be nice if you didn't have to manually configure ID before running a script. Seems like app.open should suppress all dialogs if you tell it not to open the UI.