my guess is they are expensive because they are made from different chemicals and processes from regular electrolytics... they aren't used a whole lot because there aren't that many applications that need such a large capacitance.... due to their low current handling capabilities, they are really only suited for backup purposes, and considering how cheap button-cell batteries are, they aren't always a good choice for that. However, they do have the one advantage that they can be charged many times, whereas most button cell batteries can't be charged at all, and the ones that can may be expensive, and not last through many recharge cycles.
I used to be involved in a field of robotics in which batteries were never used, only solar cells and capacitors... for that, the supercapacitors were very useful because they charged quickly but also stored a lot of energy. However, I worked at an electronics recycling place where we tore apart old electronics and sold the scrap, and only once in my entire time there (2 summers) did I find any supercapacitors in anything (they were in a gigantic old modem)