Well, did some testing and it looks like if the incoming email is marked as SPAM it does not get a vacation reply. Looking through 'man vacation', there is mention of not replying if 'There is a Precedence: bulk or Precedence: junk header.' But I did not see those specific words in the header of the SPAM emails that the vacation process did not reply to.
Well, if anything, I learned more of how some of the components work in handling emails.