Same here. I can not progress further, because I need to skull-jack a codex, and they will not appear on any mission.

I completed a mission with extraction (destroy a transmitter I think) and just kept letting them call in reinforcements with my whole squad on overwatch around the drop point until one showed up, it took about 7 waves, but it came eventually. Part of the problem is how far you are into the list of aliens though, in my experience codexes are some time after Archons.

Oh the irony! The mission after I made this post made them appear! But I haven´t encountered any archons yet, which is reaaaaally needed as my shinobis needs new swords. So yeah, the issue is still there: important enemy types comes waaaay too late.

There's a console command that can spawn a single codex if you ever encounter this issue again.