Can I use Not So Fast on bomb deathknell trigger?

Yes — you can counter a Bomb's Deathknell trigger with Not So Fast, as long as that trigger chose one of your units at that battlefield.

The Bomb's ability reads "When it dies, deal 2 to an enemy there and kill your other Bombs there." "An enemy there" means an enemy of the Bomb's controller, i.e. your unit, and a unit named in an ability is a target (Rule 355.10) — so the trigger is an enemy ability choosing a friendly unit, which is exactly Not So Fast's requirement. Countering it wipes the whole ability (FAQ #12834), so the 2 damage and the kill on the other Bombs both fail. The Bomb still dies and stays dead — only the trigger is stopped.

One gap: if there's no enemy unit at that location when the trigger finalizes, it isn't choosing anything friendly to you, so Not So Fast has no legal target and can't be played at it.