Even for acute disease, for example thrombolytics for MI, the benefits of treatment may be underestimated by looking at only 30 day mortality. In fact in some studies, adverse events or mortality may be worse in the short term and the benefits of therapy may not be revealed without months or years of follow-up.   For example, early surgical mortality may negatively impact short term results.   However, if the surgical therapy was effective in reducing mortality in the long term, with time the survival curves for surgery vs the alternative  therapy would cross,  reflecting increased survival with surgery. 

Long-term studies of prognosis require massive financial and even career investments. Some of the better known include the Framingham study, the Doctors study, the Nurses study, the country of Finland.