They better get together in Deus Ex: Mankind Divided.
I think the devs said in an interview that they weren't going to go with any particular route from HR, so she probably won't be in the game at all unfortunately. :(
Mankind Divided is now out and the fate of Malik? She's alive! In one Easter Egg in Jensen's apartment, if you go check one of the cereal boxes, you will find a toy plane and a note left by Malik.