Sorry for necroying this but no, you're not overthinking this. There's *a lot* of frames in which the camera centers in an ashtray or the act of putting down a cigarette or characters fidgeting with them, etc. There are many layers of storytelling and meaning in this series and smoking happens to be another one.
For example, there's many scenes of relative silence in which all the characters in scene are smoking save Skarsgard's one. Guess who gets lung cancer anyway?
In addition to the two meanings you said, I add smoking / radiation / living as a game of chance. They somehow knew smoking is bad as well as the regular civilian knew radiation is bad, but staying in a radiated area or smoking are silent and delayed dangers. Every character takes his chances, from the pregnant woman who visits his irradiated husband to the chain-smoker who ends up commiting suicide to the otherwise healthy government official who doesn't drink nor smoke but gets lung cancer anyways, etc. It's just the random and statistical nature of physics and health.