Should I notify people I mention in the acknowledgements section?
shall I communicate their inclusion in the acknowledgements section?


Yes, why not? It helps at building connections and improving relationships. Besides, if the acknowledged people are from a different field than yours, they might never know you've acknowledged them otherwise. 


  what will be the correct etiquette for such an email?


I don't think there is any need to be overly formal. Typically I would write something simple, along the lines of (names and facts have been changed to protect the innocent):


  Dear John,
  
  thank you very much for helping me with the problem of packing holes. I've included an
  acknowledgment in a paper I recently wrote on the topic.
  
  The paper is titled "Packing the unpackable and stacking the
  unstackable" and has been submitted to the Transactions on Painstaking
  Stacking. You can find a preprint of the paper at the address (link to, e.g.,
  arXiv).
  
  Kind regards/Sincerely/Cheers,
  
  Massimo


The above example is meant to be sent just after the first submission. In more critical cases, when I'm not sure whether the acknowledgment would be well-received or not, or if I think I might have written a wrong detail (e.g., the affiliation), I typically send a copy of the paper before the submission, asking for feedback.