This is nothing new, but coming from DEVONthink 2 newer remember how to remove tags from multiple documents in DEVONthink 3. I always look for the external script “Remove tags from selection” that was used in DEVONthink 2. In DT3 this script does not exist anymore; now you use Batch Processing:
Go to Tools → Batch Process… (or Ctrl-Cmd-B) and in the upcoming dialog select Remove Tags from the action dropdown:
Done! 
