Yasuo's W can't protect him from all his spells yes, but that does not mean he can't kill you.
Karthus has enough range to safely farm even against Yasuo's E
Karthus is a Mid-Range Mage. He has range yes, but not something like Lux or Xerath. Range also doesn't always guarantee safety against a decent Yasuo.
Karthus is also a safe pick, which also means he can't act too aggressively too much or else Yasuo's low cooldowns can and will beat his mana pool. You can afford to play safe yes, but that also means letting Yasuo farm his items, and many offensive items are more powerful on Yasuo than in most champions.
Let's not also forget that items like Hexdrinker (and even Maw exists) that Yasuo can get after his PD.