It would only count once. This is the way it is with every multi-hit move (including Parental Bond moves); once a move the Protect, Spiky Shield, or in this situation King's Shield has been used against it, the Pokemon only attempts the attack once.
So it would only lower Mega Kangaskhan's Attack once. The same goes for moves like Bullet Seed or Rock Blast; the Pokemon will protect itself from the first hit, and the attack would stop there.
I've seen this happen enough times in OU to know this for sure. Bulbapedia's page on multi-hit moves can also back me up:
Spiky Shield and King's Shield only activate once.