Correct, the higher level Storm Wave would have more base damage, and elemental damage to attacks would add on top of that.
Mana can be a problem, but is easily fixed with some Sapphires that give +2% to mana on kill.
My high end experience last league was using the Melting Maelstrom mana flask though which got a huge nerf, so not sure how well you can build mana sustain for bosses in this league.