One of the great improvements in InDesign CS4 is the completely re-engineered Links panel. This new panel shows you a lot more information about each linked graphic than in previous versions. But one important item is missing!
In InDesign CS2-CS4, if you select a PSD, AI or PDF file that contains layers or layer comps, and choose Object > Object Layer Options, you can show or hide any layers that are in the graphic file. This is called a "Layer Visibility Override."
In CS3, a Layer Visibility Override is clearly indicated in the Links panel by an evil-looking yellow eye with a red eyeball that displays next to the over-ridden link in the links panel.
In CS4, this evil eye is gone. In fact, with the default preferences, you will see no indication in the upper portion of the Links panel that the graphic has a Layer Visibility Override at all. To configure InDesign CS4 so that you don't accidentally miss a Layer Visibility Override, choose Panel Options from the Links panel menu. Click next to Layer Overrides under "Show Column". Then click the OK button.
Now, if there is a Layer Visibility Override applied to a graphic, you will see a "Yes" displayed to the right of the file name in the Links panel.