Although his weapons are on display in the GCPD, Deadshot doesn't physically appear during Arkham Knight. However that's not to say that the villain still doesn't have a hand in trying to take you down, as his name is actually engraved on the RPG shells that are fired by the tanks throughout the title.
When you're being fired upon in the Batmobile, if you enter photo mode and check out the missiles, you'll notice that they're all engraved with the villain's name. You'd never notice if you were just regularly playing the game, but it's a reminder that Batman's enemies are always out to get him, even if it's only by supplying another villain with a heap of explosives with their name all over them.
As a bonus entry, Halo 3 did the same thing back in 2007, engraving a name on every single bullet that was fired, a fact that was only discovered when players stumbled across it while messing around with the Theatre mode.