Applescript to dismiss all "drive not ejected properly" notifications. This can be run as a script at the terminal, setup as a cronjob, run through Alfred, etc.

dismiss-notifications

#!/usr/bin/osascript

tell application "System Events"
  tell process "NotificationCenter"
    set vWindowCount to (count windows)
	if vWindowCount is 0 then
	   return
	end if
    set vWindow to window 1
    set vNotificationContainer to (UI element 1 of scroll area 1 of vWindow)
    set vNotifications to (groups of vNotificationContainer)
    set vNotificationCount to (count vNotifications)

    repeat with vNotificationIndex from vNotificationCount to 1 by -1
      set vNotification to (item vNotificationIndex of vNotifications)
      set vNotificationTitle to (value of static text 1 of vNotification)
      if vNotificationTitle is "Disk Not Ejected Properly" then
        set vDismissAction to (action 3 of vNotification)
        perform vDismissAction
        -- Executing the dismiss action too quickly causes some of them to be ignored.
        -- Adding a delay to allow the UI to catch up.  Anecdotally, 0.1 doesn't appear
        -- to work but 0.2 does.  0.5 is used to give a time buffer.
        delay 0.5
      end if
    end repeat
  end tell
end tell