Yes, it has. The Assassin and Inquisitor must be from the same codex.
If one includes DH and WH allies, they could have one Elite from each. The same would apply to HQs if the player had three HQ slots available on their FOC.
From the FAQ.
In other words? No, you cannot take an assassin from one ally's elite slot after unlocking it from another ally's elite slot. You MUST purchase an HQ slot inquisitor if you want to ally in an assassin, and it MUST be from the same codex as the assassin entry you're using.Q. Can an Officio Assassinorum Operative or Daemonhunter Deathcult Assassin be taken as an ally in an army that only has a Witch Hunter Inquisitor (or vice versa)?
A. Witch Hunters and Daemonhunters are discrete types of Inquisitor. The Officio Assassinorum Operative or Deathcult Assassin may only be taken in an army that has an Inquisitor from the same Codex.
The mouth of the Emperor shall meditate wisdom; from His tongue shall speak judgment