Consider, however, that it took a advanced communications and scanning station like Epsilon IX (and at close range too) to determine that there was something inside V'Ger and not just an external Energy Cloud ("I have a null reading at the centre of the Cloud, "Definatly something inside there, but all scans being reflected back")
The Klingons couldn't have possibly determined that there was something inside the cloud...
The Klingons suspected there was an object at the center of the cloud. Likewise, all Epsilon Nine could detect was a "null reading" from which they surmised there was "something inside there", essentially the same thing the Klingons did. The Enterprise didn't even attempt a scan, fearing it was scans that triggered the attacks on the Klingons and Epsilon Nine (it wasn't).