I do believe that they are aware of each other existence, Aatrox would know about the guy who killed one of his kind (Regardless if Jax had help), specially considering that they were enemies during the war of Icathia. However im not sure if they know that the other is still alive.
Anyways, I dont think that Jax is being pursued because he is clearly not human... and so far we have only seen Darkins with Human hosts. After all, Darkins take host in order to reach a similar form to their original Ascended forms and their original forms are based on their human forms (assuming that there are no vastaya, yordle, troll, etc ascendeds)... so, the extra eyes and lack of some fingers could be a problem for Aatrox, regarless if he considers Jax "worthy" or not.