Should I shuffle the Visage tokens after an investigator gets devoured?
From page 9 of the Innsmouth Horror rulebook:


  Remember, leave visage tokens faceup after revealing them 
  unless either Ghatanothoa’s face is revealed or there are 
  four visage tokens faceup after revealing the new token.


So while it doesn't explicitly tell you to turn them facedown and shuffle them, I'd say it's clear enough. So yes, no freebie clue harvesting after your poor friend gets devoured!