I use a drive cage to plug in and out SATA hard disks on a Windows 8.1 64 bit system. The drives are recognized as standard hard drives, so removing them even if all writing / reading activity has stopped the drive is still spinning.

How does one designate the drive as removable so it can be stopped? Will trying to connect them as eSATA do this and not cause them to spin down and not be recognized while still being plugged in?

You can try looking in the BIOS to see if you can specify specific SATA ports to be used as removable or hotswap. Does it hurt to try the eSATA option to see if it works?