It really shouldn't affect the hard drive unless you drop the drive while installing the battery. When you replace the battery on your 30 gig, there is no need to remove the hard drive.
The battery is located on the back upper hand of the IPod, near the headphone jack. There is no need to unplug the hard drive.
You need to be careful when you are taking the IPod apart. I accidentally cracked my screen when I was trying to take my IPod apart with the proper tools that came with the battery kit. I needed to replace my headphone jack, the screen and the battery.
I had to replace the screen twice because the first replacement screen was faulty.
Backing up your music is highly recommended, but when I got my IPod back together, everything worked fine and still working.