Depends. Cain was a commissar who knew about chaos, but wasn't always supposed to know about chaos and that was mostly due to working with an inquisitor(the necrons were also a big secret at one point) Obviously the higher ups with any length of service will encounter them at some point, but when you've got groups like the grey knights who will insist that everyone exposed to chaos in any way needs to be mind wiped or purged, there's no consistency. And of course the naval command officers who have to work with navigators know, because the navigators and astra telepathica are a whole other group of imperium citizens who knows things that most don't.I think that if you are high enough (commissar or commander) you get the debriefing that chaos is a force rather than nebulous traitors with magical rituals.
Unfortunately the truth is that it's retarded writing. Since everyone familiar with the space wolves knows about their psykers and the chapter's 10,000 year beef with the thousand sons(nevermind the invasion by the thousand sons), and on and on. This is the same retarded writing that at one point had grey knights slaughtering sisters of battle to bathe in their blood to try and help ward them against demons... yeah don't try and put much thought into that, the writers definitely didn't and it's a prime example of grimderp.Also my headcanon for the GK and Space Wolves mind wipe was that the Space Wolves might accidentally came to know secret information about the GK that puts them at risk.
The inconsistency in knowledge about the enemies of the imperium is interesting at times(when the writers aren't retarded), and allows shit like tau having an easier time influencing planets, rogue traders getting up to shenanigans, etc.