The Inquisition were entirely connected to the Church, and, given the player kind of destroys it's power base (exposing both the lies the Church was built on, the rampant corruption within the organization itself, and that.. whole thing with the Archbishop and the Heavens Ward...), the Inquisition technically no longer exists in any meaningful form.

They were also well known for working in secret so again it's pretty obvious why apart from that kangaroo court that Alphinaud and Tataru were caught up in (and some lore padding that started the DRK quests off), that the player has actually little contact with them.