Disk utility shows unattached external HDD
I seems found a work around to avoid reboot. After eject the Time Machine volume in the normal way, I open disk utility and eject the physical drive there, and wait untill the disk LED indicator shows that it is in sleeping mode (slow blinking) and then disconnect the drive. Now the physical drive is gone in disk utility, and I can close/sleep the MacBookPro. Next time when connect the drive, it will show up normally.

I wonder if this is because OS X sierra didn't handle the ejection process for encrypted drive properly.