Possibly, I was able to install my SSD in the Optical bay, the HDD holds media and some lesser-used apps, if not needed it spins down and I find I get greater battery life than before.
If I am not accessing the media on the HDD then it spins down after a period and stays off. Whether your drive spins down will depend on the drive, what is on it, what your energy saver prefs are and whether it is in the main drive bay.