I think you hit the nail on the head with your question.
Zyprexa decreases (for some people) hallucinations, delusions, and mood disorders. Sounds great, however, if taken over a long period of time (and that's how all APs are intended to be taken) Zyprexa causes a significant increase in blood sugar (hence the class-action lawsuits against it), which leads to hyperglycemia and diabetes. Zyprexa also significantly increases the risk of hypertension and cardiovascular disease.
All of the atypical APs increase the risk of serious health problems if used over a long period of time (20 years? 30 years?), so I'm not singling Zyprexa out. On the flip side is a medication that ameliorates serious mental health problems, so it seems to be a damned if you do, damned if you don't situation.