One of the systematic changes in MoR is that things which are sufficiently powerful are artifacts, and things which are artifacts are sufficiently powerful: The Marauder's Map was originally devised by Slytherin as part of the creation of Hogwarts and only slightly twisted by the Marauders (Ch. 25), and the Cloak of Invisibility is now in a class of its own compared to standard invisibility cloaks or Disillusionment (Ch. 54).

Rowling, of course, wrote that thing with Moody's eye before she decided the Cloak of Invisibility was a major artifact. So if Moody's eye can still see through it in MoR, it's going to be because either Moody's eye is also a major artifact, or, more likely, a specialized artifact devoted to seeing through invisibility (a specialized, specific artifact can defeat a generally more powerful artifact if the specialization is narrow enough).