So, enhancers have mastery that increase fire, frost and nature dmg by x%, now, my question is, does it increase dmg done with elemental blast (since it also does fire/frost/nature dmg) three times or just once?
Just once. The Fire/Frost/Nature simply are qualifiers. If it is any one or combination of the three, it gets mastery's damage.
Any spell/ability that has a potentiality to include several elements won't benefit multiple times, it acts as one