This issue was reviewed recently in Cirulation. The HDL story is not over. Some of the points of the review:
The epidemiologic association between low HDL levels and cardiovascular disease is very strong.
The risks associated with low HDL can be moderated by nonpharmacologic means.
The main controversy regarding HDL concerns pharmacologic management. Early studies with niacin (e.g. the Coronary Drug Project) and fibrates (Helsinki I) showed reduction in cardiovascular events. However, several more recently conducted trials failed to show improvement attributable to pharmacologic treatment directed toward HDL. This is in part attributed to confounders such as concomitant statin treatment.
Questions for future and ongoing research include patient selection for treatment and new approaches in the pipeline.