So I’d absolutely say that all of those things would be detectable - but just because you can see something doesn’t mean you will notice it 100% of the time.
Maybe the Undead could use visual cover or smoke to shield themselves from the Sniper’s vision, because the ‘glow’ around them only becomes really noticeable in large numbers.
Maybe more powerful supernatural effects are more pronounced, so a Hexed might be almost unnoticeable whereas a Broken will light the world up like a distant volcano.
Maybe the Sniper has to be focussing on their supernatural vision for it to be 100% reliable - it’s an alchemical construct, after all - and so has less use of it when their other eye is open.
Maybe powerful supernatural effects in an area can make less powerful ones difficult to spot. If you’re standing near an Old Empire warding stone, you might not spot that the refugees you’re helping are all Hexed because of the magic leaching from the Stone.
Maybe the eye reveals the true nature of the supernatural - and the Undead? Their true nature is unpleasant. Stare too long and rely on the eye too much, and your Sniper might be on the first Orite locomotive to Traumaville.
(Conversely, maybe it doesn’t - are those townspeople approaching the Legion position Hexed? Or have they just been anointed in the local blessing pool? Is that the power of the Twins, or Breaker? Can your Sniper tell? Are they gonna take the shot anyway?)
BoB seems to have a very strong focus on the idea that there ain’t no free lunch, especially with magic, and so while I think the one-eye ability should be powerful - the character’s made a very Odin-like sacrifice for knowledge, after all - I also feel it should have risks for its use and not be 100% reliable.