Yeah, that's one of those weird issues; if the Shivans knew the information was out there, why didn't they just send an Azrael full of Shivans down to the planet sometime in advance in order to destroy the information repository in detail? Simple arrogance/overconfidence?
I do have a sub-theory that the Shivans somehow developed some sort of loose alliance/non-aggression pact with the Hammer of Light(obviously some time after the Ramses, and La Ruota della Fortuna), explaining how HoL forces to continue to exist in Shivan-controlled space seemingly unimpeded, and in fact seem to come to back up the Shivans on at least 2-3 occasions(Reaching the Zenith, Black Omega, and of course, the Prophecy in The Great Hunt), and the Sekhmet(Shivans sharing primitive Nahema schematics?).
In this case, the HoL in Altair picked up the scientists' broadcast, and told the Shivans the contents of the transmissions. It's possible the HoL may not have known how significant it was at the time, but the Shivans may have known what the Ancients had discovered about them prior to their demise.
OTOH, the FS Ref Bible did point out the similarities between the Ancient and Vasudan languages, so it's possible that the Shivans, over the time spent eradicating the Ancients' multi-galaxy empire, learned to 'decode' Ancient, and were thus able to understand and/or communicate Vasudan. The Shivans could have simply considered the HoL irrelevant for the moment, and ignored them, as HoL forces seemingly never engage the Shivans(based on the how the Ramses chooses to just roll over and die when the Taranis attacks).
Without this(or significant parts thereof), there just doesn't seem to be a reason to send the flagship of the Shivan armada after a couple transports and a science cruiser(unless they were just trying to kill Alpha 1

).