Magian Blood

How does Magian Blood major virtue interact with the penalties for learning supernatural abilities you don't possess? For example, if you have a hermetic magus with Magian Blood connecting Magic Theory, Second Sight and Whistling up Wind, but no virtues giving the latter two, does every xp point get turned into zero?

Pretty much, yeah. You should have developed Second Sight naturally at some point, but you didn't, so that effect essentially fizzles.

It's a very strong justification for getting Second Sight or Whistling up the Wind from your first positive Twilight, though.