The compounds in dark chocolate appear to be highly protective against the oxidation of LDL. In the long term, this should cause much less cholesterol to lodge in the arteries and we should see a lower risk of heart disease over the long term.
It turns out that we have several long-term observational studies that show a fairly drastic improvement. In a study of 470 elderly men, cocoa was found to reduce the risk of cardiovascular death by a whopping 50% over a 15 year period.
Another study revealed that eating chocolate 2 or more times per week lowered the risk of having calcified plaque in the arteries by 32%. Eating chocolate less frequently had no effect.
Yet another study showed that chocolate 5+ times per week lowered the risk of cardiovascular disease by 57%.
Of course, these 3 studies are so-called observational studies that can not prove that it was the chocolate that caused the reduction in risk.
However, given that we have a biological mechanism (lower blood pressure and oxidized LDL), it is plausible that regular consumption of dark chocolate can in fact reduce the risk of heart disease.