The question is effectively: "can SATA controller tell the difference beween SATA port connected powered down drive and SATA port not connected to anything?". I think the answer is no, so you should be fine.
(1) SATA cable only has 2 differential pairs, so there is no CPD or any other out-of-band information that can be used to tell if drive is plugged in.
(2) One arbitrary SATA PHY datasheet suggests that receiver only cares about presence of differential signals, and not about common mode or transmitter resistance: http://electronix.ru/forum/index.php?act=attach&type=post&id=607
SIGNAL_LEVEL_VALID output from the PHY indicates that the differential
input signal exceeds the squelch detector threshold.
(3) The same datasheet has no mention of receiver detection on transmitter part.
I am going to guess that other PHY's behave the same way, and thus you can safely power drive off while leaving it connected.
This said, are you sure this is what you really want? There may be easier alternative solutions:
- If your goal is to save power / have less heat or noise, you can always unmount, then use
hdparm to put the drives into sleep mode. No hardware required.
- If your goal is to protect from viruses, then the viruses can still infect the drive while the backup is running. It will be safer to make a mini-NAS with access over the network.
- If your goal is to protect hdd from lightning strikes / power surges hitting the computer you will want to use USB or Ethernet enclosures -- this way, a power surge will burn out USB/Ethernet port on the enclosure, hopefully leaving the drive intact.