Yes, you will, though not as main characters. Their specific story has ended, but they remain important members of the Shadowhunter world and play a big role in The Dark Artifices and the Wicked Powers. You can also see them in the short story collections like The Bane Chronicles, Tales from The Shadowhunter Academy, and Ghosts of the Shadow Market.
Magnus and Alec, of course, have their own whole series — the Eldest Curses. Check it out!