Right now, projectViewer shows when a file has changed (tiny disk icon) and when it's open in a buffer (underlined)
A logical next step is to integrate hypersearch results, for example making files that contain a match bold. Or different background color.
Whlie an interesting idea, there doesn't seem to be a way to be notified of hypersearch results (just to request a hypersearch). So this can't be implemented against the current jEdit code.