In the parent article they said they switched because of cost: "When Hitachi drives got too expensive we switched to Seagate and Western Digital. When internal drives got too expensive we turned to external drives. When hard drive availability became an issue we turned to Drive Farming."
From their article on v2 they said: "The Western Digital and Seagate equivalents we tested saw much higher rates of popping out of RAID arrays and drive failure. Even the Western Digital Enterprise Hard Drives had the same high failure rates. The Hitachi drives, on the other hand, perform wonderfully." http://blog.backblaze.com/2011/07/20/petabytes-on-a-budget-v...
There are other articles where they mention that they do testing and some brands perform better than others.