I'm not sure how it would affect a top security foreign affairs clearance, but I have gotten FBI clearance to work with agents of bioterrorism (certain bacteria and moulds) with being BP1. They did ask if I had ever been "committed to a mental institution", but it was in the legal sense, not just having been hospitalized, even if it was involuntary at first. (Formal court-ordered commitment hearing type commitment is what they were looking for.) I also had to have a full Federal background investigation for my job at the VA, but I didn't have any high security clearances there. I had medical security clearances, but not special intelligence clearances.

I think it depends on your history. I can't see them being able to deny you based only on the fact that you are bipolar.