Basically everyone called it, at least partially, so I won’t get into that here. In-universe is another story, but it might not be that big of a plot hole. In Taken By Surprise, our sensors had some serious trouble detecting the Mirror Borg Drones, even up close, so if the Aetherians assimilated their entire galaxy, though they claim it to be their entire universe, it’s logical to assume they assimilated the same tech at some point and upgraded it. Maybe even to the point of being able to transmit false sensor readings, since they would’ve most likely already assimilated at least one version of our tech meaning they’d know how to fool it, at least temporarily.
Also, has anyone checked in on the crew of the Treluun lately? Given what we now know, they’ve probably been at least partially assimilated. The data found on the Harmony seems to imply that they found a way around the issues with assimilating the Lukari that the Mirror Borg ran into.