If his disappearance is actually something, I'd say his recent adventure has awakened him from centuries of self-deprecation and he's looking for something or someone to take the fight to Azshara.
Farondis was underdeveloped in Legion, but I think he still has the potential to become the iconic "night elf rebel" who dared saying no to the queen when everyone else was madly in love with her and the power she provided. He could be a better Illidan. A smarter one.
He could be researching the MacGuffin of the next expansion, the weapon/power to defeat the naga and stop an invasion. Or maybe he's just gone somewhere to reflect on his actions and what happened to his people, to regain strength and motivation to finally do something.
Or maybe he's just sick of being hated and has become a hermit in some cave.
In any case, I very much doubt he's gone and joined his biggest enemy.
Edit: Or yes, he could have been captured by Azshara. The sad part being that nobody has cared enough to tell us to go save him.