OS X is supposed to optimize the location of files on the HDD, as least it used to. So if OS X is putting the Windows partition in the location marked as the fastest read/write spot on the HDD, that's a failure on Apple's part.
As to my source for Yosemite handling terribly on spinning HDD's? Just experience.
Yosemite is blazing fast on old hardware with an SSD, but if you put it on newer hardware but with an HDD - such as a new 27" iMac that has a 1tb HDD - it gets very slow, very fast.
At work, I have a mac with 8gb of RAM and a quad core CPU - monitoring my CPU usage shows it's never over 50%, and my RAM usage is around 6gb max, so I'm not really resource constrained no matter what I'm doing... but the OS is just slow. Computers with slower CPU's and less RAM (such as the new MacBook) run Yosemite faster though. Coincidence? I think not.
I don't think that HDD read/writes have slown down, but rather OS X tends to cache much less aggressively, so the OS needs to do more read/writes, which has the "side effect" of making your old computer feel slower that it would otherwise.