Shutdown without and close all windows from terminal
I am searching for a solution to the same problem. I have not found a nice solution although there is a hacky one here which in short is:

Disable saving application state:

rm -r '~/Library/Saved Application State/*'
chmod -R a-w '~/Library/Saved Application State'


Disable 'Reopen windows when logging back in':

defaults write com.apple.loginwindow TALLogoutSavesState -bool false
chmod a-w ~/Library/Preferences/com.apple.loginwindow.plist
sudo chown root ~/Library/Preferences/com.apple.loginwindow.plist


See the provided link for more details.

But I really hope there is some better solution to this ? In my case the problem is that I have a mac in a server room that automatically runs a script in a terminal window. This machine can be rebooted remotely. But thus every time it reboots it keeps the old terminal window and opens a new one, so if I have rebooted it 10 times there will be 10 terminal windows open where only one is in use.