A cyber penetration that does nothing other than lurk and gather information is very different from one that attempts to blind you.If this were true constantly we wouldn't have a Singer problem considering they are themselves cyber entities and one of our first discoveries in the Discord mechanic was that a number of our ships were compromised and it wasn't immediately clear which ones.
One is attempting to keep a low profile, the other is basically clashing cymbals as it walks.
And Starfleet actually has experience with cyberattack, as compared to peoplejacking.