Off the top of my head, below are some questions I have heading into the next season (No way I'm reading the books). I'm sure the show will provide some answers in the future.
1) why did the govt need to erase all history? Obviously, it's nefarious as shit, and they want to hide the origin story of how everything went down, but what exactly happened that needs to be covered up?
2) why so many silos? Capacity?
3) What's the blinking key fob that Nuke Laloosh has? Keys to the "real" server room? Is 18 the number of their silo?
4) where does the giant door go? To another silo?
5) what exactly is the syndrome? What happens beyond the hand cramps and tremors?
6) So did the founders plan for "head of IT" to be the real leader all along? How is that succession plan handled? Through the half-ass shadow thing?
7) Why do the silo denizens/govt need cleaning of the camera? I think it's so they can see the outside world and how dangerous it is. The govt needs this to prevent potential rebellion. No outside view might convince some cowboys to call bullshit and open the hatch.
8- why are pulleys and elevators outlawed? Likewise, they couldn't have a machine or simple windshield wiper do the cleaning?
9) I'll stop for now, but in the lesbian sex scene, what did the tattoo on Rebecca Ferguson's labia mean?