OK, here's the story....
The Toshiba PC Card Hard Drives will spin down if not accessed after a short period to save power - they are SMART in this sense. If you are accessing the drive a lot then you will see your batteries run down faster but we are not talking major power drain.
From my experience with a Toshiba 5GB drive on both a Jornada 720 and Intermec 6651 the drive does have a *significant* but not destructive impact on battery life. Used infrequently, i don't think you'll notice that much.
You should probably remove the drive from the Jornada when not in use though just to prevent unecessary spinning up of the drive.
These comments are for the Toshiba PC Card Drives but as far as I'm aware the Kingston ones are pretty much the same hardware.
Opening files on the drives is not much different from opening files from CF or internal memory except that if the drive is 'asleep' it will take a couple of seconds to power up.