Yup, that's because Blastbones uses a skill to blow itself up. You'll notice in CMX that the damage of Blastbones isn't called "Blighted Blastbones", it's called "Blighted Blastbones Detonation". It's an ability that the Blastbones itself is "using".

The Blastbones itself is being silenced in the Negate, and is therefore prevented from "casting" its Detonation ability.

You'll find that this is the same for other Necro Pets. Damage from the Skeletal Archer/Mage/Arcanist isn't referred to by the skill's name, it's referred to as "Deathbolt", which is an ability "cast" by the minion. Spirit Mender is the same - it "casts" an ability called "Reconstitute".

This is also why you cannot proc sets with any of these Necro pets, and why Necro pet damage/healing doesn't show up on the scoreboard. The player is not the source of these abilities; the pets are. They aren't tracked by the scoreboard because you aren't the one dealong damage/healing, and they cannot proc sets as the pets are not the ones wearing the set.