1. The logic you describe happens on opening files only, it doesn't require running every couple of seconds. Also, if Denuvo would use that kind of protection only, it would be super easy to hack it by removing the loader and using decrypted files. Instead, as written in article, Denuvo uses additional checks during runtime to validate fingerprint somehow. I'm not sure whether this requires reading any files or not. I guess some hooks do it, while other don't
2. The decryption on opening files also could degrade performance greatly when files are loaded. You could check this discussion
3. The effect of such DRM on a particular game also could depend a lot on the game itself. Civilization games traditionally read and load files constantly as they have to juggle their assets. If that's the case and Denuvo constantly decrypts those files, this could cause much bigger performance degradation than in a game where files are generally loaded on level switch only
Of course, those are just theories and for me Denuvo is not a game breaker, but its use still raises some questions.