The hard drive parking its heads after activity or/and a short length of time is also a form of advanced power management that's used to conserve power and reduce heat. Only qualm I take with it is that it causes said heads to park more than I think they should, which might end up in wear and tear on the heads (and therein an unnecessary increase of load_cycle_count, or rather the unloading and loading of the heads) and premature HDD death. I agree that Western Digital (along with Seagate, possibly even more, in my experience - Western Digital hard drives might park their heads after 8 seconds of inactivity, but modern Seagate drives have for me after 2-3 seconds with APM on!) are quite aggressive with this approach, though they're not the only HDD company to do this (but it would depend on the model as well). If it's a Scorpio Blue or Black drive (due to being a laptop drive) you might be able to download a third party app like HDDScan or CrystalDiskInfo and disable APM (which should do away with intermittent clicking), though it might result in a slightly higher idle temperature for your hard drive due having the disk spin in a more unending manner. However, not all Western Digital hard drives can be recognized as having APM by such applications, in which case you would have to download an executable known as widle.exe and write it to a bootable disk, and you could disable the "idle timer" that way, though that voids the warranty and firmware. But make of note that Windows applications like the aforementioned do not permanently change the settings of the hard drive (you would have to turn off APM again after rebooting... you could try writing something like Hitachi Feature Tool to a permanent disc if you wanted to permanently change it but I don't know how well that supports WD hard drives so I'm not sure that should be risked).
I'm not necessarily suggesting doing any of this to begin with as I believe there is always a risk with messing with low-level hard drive settings along this nature, though if you know what you're doing (which I imagine you do), you should be fine. If the clicking doesn't bother you that much, I think you would be alright continuing as you are. Then again, if the hard drive once froze on you during transfer, I would worry about it being defective. D: But it sounds like you're going to replace it anyway, which might be ideal.