The first thing that pops into my head isn't a standard fantasy but 'The Girl with the Dragon Tattoo'. Lisbeth Salander's not a hired killer, but she operates with that same brutal, uncompromising precision when pushed. Her empowerment is entirely her own messy, antisocial, brilliant creation, and she dismantles systems instead of just targets.
For a more traditional take, I keep going back to Celaena Sardothien from Sarah J. Maas's 'Throne of Glass' series. Yeah, it gets more epic fantasy later, but the core of her is this assassin who defines her own strength through survival, refusing to be anyone's weapon. Her power is as much in her defiance and her love for her chosen people as it is in her blade work.
Then there's Mia Corvere from Jay Kristoff's 'Nevernight'. She's literally trained from childhood for revenge, and her empowerment is a dark, bloody, and deeply flawed thing. She's powerful, sure, but the books constantly question the cost, making her strength feel earned and terrifying, not just a cool trait.
Honestly, I look for assassins whose power isn't just physical prowess but a complete reclamation of their own agency, often against systems designed to break them. That's the real hook for me.