It will hit. Attacks in the game are divided into targeted projectiles (Malphite's Q, Ashe's Basic attacks), AoE skillshots (Malphite's ultimate), Semi-Skillshots (Yasuo's Q, Ezreal's W), Skillshots (Nidalee's Q, Ezreal's Q). The only thing that can stop an ability from connecting is the ability not being in the area of effect.
Areas of effect are calculated by hitboxes, which measure two axis, x and y. In other terms, it's what's for your character Front-Back, Left-Right. Being airborn only moves the character's portrait, the character will not be moved up (as there isn't a Z axis), hence that is why it will still hit.