How do I manually "shut down" an hard drive without plugging it out?

I am connecting 1-2 hard drives via E-SATA. Using Windows, is there an option to force "shutting down" that hard drive (until it is needed again)?

What you're looking for is to 'spin down' a drive. Here is a similar question.

If you want to disable drives with the command line, you can use DevCon:

devcon disable <hardware id>

Using the device manager:

Right click on disk > disable

https://www.meinfach.net/revosleep/

or

http://hddscan.com/

Personally I prefer revosleep

You can't do it with Windows directly - the only option you have is through power options but typically this turns off all hard drives at once - there is some specialist power option software (I won't link as links become outdated, just use a search engine).

Or, as you're using e-sata I assume this is external - you could get external sata boxes with power buttons but as per my comments I think the powering up and down would cause more damage than leaving a disc idle.

FYI typically even by disabling the disc in Device Manager does not stop it from using power nor from spinning. If it has power, it is on!