What we know about the Ancients is mostly due to FS1's cutscenes and Intel entries, plus the whole Knossos deal in FS2. We have sketchy information on what archeologists have found in Altair, and we have to assume a significant chunk of that information has been classified to the highest levels.
Also, ETAK demonstrates that even though the GTVA had access to certain knowledge, they decided to bury it and focus on something else. They had the means to start a project that would have enabled them to communicate with the Shivans, yet they cancelled it, regardless of its potential benefits. In a similar fashion, they may have disregarded precious hints given by the Ancients on the true extent of the Shivan fleets. It took Capella to drive them to mental sanity, because no matter what the GTVA would do, 80 Juggernauts are well beyond their capability.