How to safely eject a volume when the icon has disappeared?
If a disk has been ejected via Finder and the icon has disappeared but you feel it hasn't yet, then here are some things you can try:

Does it show up in Disk Utility? If it does, eject it from there and if not, then it's safe to unplug.

In Terminal, diskutil list -- It the device is not listed then it's safe to unplug it. If it is listed use e.g. diskutil eject diskN where diskN is e.g. disk3, then follow it up with diskutil unmountDisk diskN.  If it doesn't unmount you can use: diskutil unmountDisk force diskN