Thanks for playing! If you ignore a threat and let it expire, it does increase the threat level, so that's a reason to engage with at least some of them, but they are indeed otherwise optional for the most part. The only thing that you can't produce passively is moscovium, which is then needed to produce livorium, which is required for the later improvements that let you win the game (the security buildings). Of course none of this is explained very well in the game, which is on me haha.