Some drives spindown after a predetermined time if they are not commanded to stay spinning. This is a known issue and affects quite a few devices. This is generally an editable setting but you will need to get the correct software for the hard drive and manually change the setting.
Only one port on the Wii is used for USB devices running off cIOS.
The WD devices do seem to be the best out there, I have the 320GB USB powered passport and it works great.