I've done just about every chest revealed by timed Deepsight that I could find between two characters now (for Disbelieve) and have only 2 that have counted towards the secret since I began playing the season when it came out. Today I've been consciously out looking for these and can confirm that they're not changing the count. Predator of Predators is bugged in the exact same way. This is currently broken and preventing me from completing the Chief Investigator requirements to earn the Fundament Shell.