Does "not so fast" counter both Deathknell triggers of Ruined Rex with Karthus on the field?

No, "Not So Fast" (assuming you are referring to a card effect that counters a triggered ability) will not counter both Deathknell triggers.

Why it counters only one

According to RiftJudge FAQ #9480, when you have a unit with a Deathknell ability and you control Karthus, Eternal, the Deathknell triggers twice (the base trigger plus one additional trigger from Karthus's passive ability).

These two Deathknell events are treated as separate triggers on the chain.

• Separate Items: Because Karthus's ability is a passive that adds an additional instance of the trigger to the chain, each trigger is an individual item.
• Targeting: If a card effect (like "Not So Fast") says "Counter target triggered ability," it targets only one specific instance on the chain. Using it once will only stop one of the two triggers; the second trigger will remain on the chain and resolve normally.

To stop both triggers, you would need to use a counter effect twice.