Cost is the most common reason not to use carbon that I have seen. And that is replacement cost after it breaks. I don't believe they are any more prone to breakage than aluminum when installed correctly, but if they do break obviously they are more expensive to replace. There is usually some discussion about the limited benefits of the vibration damping since you're running lower pressure tires.
That said, I run a set of FSA K-wings and have been very happy with them. And I just find that those bars in particular fit my hands very well and allow for comfortable positions.
I am building up a super light rig and contemplated this for a while. I ended up going with a scandium stem and aluminum bars. Google "carbon handlebars cyclocross" and you will find some crazy pictures and horror stories.
Are you going to unwrap the bars and inspect them every time you crash? Can you afford to replace them when you do crash? Stuff happens. You'll drop a bike over the barriers or get trampled during a start.
And perhaps cost is no issue to you. But if it is why not put the money towards something else that would actually benefit your performance? Do you already have a set of Typhoons and Rhinos? Got a coach? Why not hit a USGP?
Most carbon stems are aluminium with a cosmetic carbon wrap and in the case of the ritchey wcs 4 axis matrix stem is heavier that that alloy version (according to excel sports boulder). Bars on the other hand are kind of a different beast all together. You could get a 185g carbon bar for $324.99 and up or you could get a 210g aluminium bar for $109.95 +/-.
OK, so this discussion brings up a question that I have. Looking at the abundance of carbon in cross and mountain biking, it's hard to think that there is still some question of the reliability of carbon parts. Carbon is everywhere in Cyclocross. Frames, wheels, forks, etc. Is there a specific reason that handlebars are considered more of a problem than other carbon parts? Or do a lot of people think that carbon in general is a bad idea for cross?
If you're made of money, there's nothing wrong with carbon parts on your cx bike, but I really do think it's a waste. Carbon parts for road racing makes sense, because the races are much longer, and over a long race, counting grams might make a difference. CX races are so short, that the weight of your bike doesn't really matter that much overall. I don't think it's a reliability issue, but it seems like burning money to pay double for a carbon part just to lose a few grams.
You probably pick up enough mud in one lap to negate the weight savings.