Disabling all oribital buildings for three minutes is nothing to scoff at. For three minutes your enemy will not be able to get resource income from that planet (IDK about tax income), build new ships, research the same levels of techs (since his labs are effectivley "dead"), get trade income, refinery income, or spread culture.
My buddy likes to play as Advent and masses culture centers on border worlds, a quick shot from the Kostura disables them and allows my cap ships to leave my gravity well without fear of my planets being overwhelmed from the loss of the capital ship culture repel bonus.
It can make a fight swing in your favor. The cannon disables all hostile units for 15 seconds, plenty of time to take out many of the most dangerous ones before they come back online.
It is actually more useful than the Novalith, since that late in the game you are bound to have many planets and losing one is no big deal. But your ability to churn out new ships or culture spread being shut down for three minutes is not plesant.