If you play the witch and then unite with another witch, do you gain a total of 12 Honor which makes the Unite reciprocal or 9 in which case the extra 3 only comes from triggering of the first?
You would receive 12 Honor. You get 3 Honor just for playing the Everbloom Witch and each would give you an additional 3 Honor based upon it's Unite effect.
Second question: if you play a hero and his day/night ability would trigger later in the turn due to a shift of day night do you get the bonus?
No. Day and Night status is determined when the Hero card is played.