No, it's not just a marketing ploy. The watercooling tubing is much more flexible, and can bend tighter without kinking. Some tubing, the Primochill LRT for example, is also anti-microbial, so you need to get any additives to prevent algae build-up in your system. Little things like that account for the higher cost, and they can go a long ways towards making installation easier. But you won't see any actual performance benefit between the different kinds.
In my own experience, the hardware stuff is rarely circular - it's usually a little flattened, since it's been sitting wrapped on a roll so long. And a lot of it kinks if you so much as look at it funny. But in a pinch, you can certainly use it.
__________________ i7 2600K | ASUS Maximus IV GENE-Z | GTX Titan | Corsair DDR3-2133 |