How can I clean Unknown item of kind Unknown from my Account startup items system preference pane?
This appears to be a bug in OS X High Sierra (it may affect other versions too) and has been bugging the crap out of me for the past few weeks. I finally managed to find a solution, thanks to a post I made on this Github issue. Try this solution.

Basically you will want to remove the file $HOME/Library/Application Support/com.apple.backgroundtaskmanagementagent/backgrounditems.btm. Then reboot.

Note that that this will remove all Login Items you currently have set up so be sure and make a note of all of the apps, volumes, etc. you currently have set to auto-launch at startup, because you will have to re-set them up. But this definitely got rid of all the "Unknown" items for me.

The other alternative is to set up a new user folder and migrate in your other files, but having a backup and erase install / migrating in from a backup is a great solution as well.