Switching a USB HDD on and off
If your HDD enclosure is designed correctly (which is likely, since it likely will be using a standard trusted bridge IC), removing VBUS should cause the drive to disconnect, and upon restoring VBUS the drive should get fresh enumeration. Without VBUS nothing should happen. At least there is no danger to try VBUS off and on. 

I personally just turn off the entire 12V DC power with a switch. 

I wouldn't advise to make "USB 3.0 switch", it is a failing proposition. It is doable, but would require to carefully build a PCB with impedance-controlled differential traces and good qualified USB 3.0 connectors with proper fan-out, it will take a good effort.

ADDITION: Correctly designed USB device must signal its connect event (start USB 3.0 termination detect or D+ pullup) only if VBUS is present, regardless if it is self- or bus-powered. The rule is "no VBUS - no connect". In all cases. See Section 7.2.1 and 7.1.5, USB devices "may not provide power to the pull-up resistor on D+/D- unless VBUS is present." So this old article is correct.