[ma2t]

Yes and no. When trying to show quantitative data in terms of areas or angles, then you are spot-on: same issues. But these plots, or chord diagrams more generally, are often used to show relationships (like translocations, inversions or duplications in genomes) in context of other landmarks. This use is common and less troublesome. A real problem with Circos plots is that it's so tempting to keep adding additional tracks of "information" that plots get ridiculous. It becomes like staring at the Voynich manuscript: uninterpretable but so compellingly pretty it must mean something.