My understanding is that, while the CNP is obviously functional and works as designed, the CNP's backdoors was what made it dangerous. Whether the CNP's backdoors allowed activation of a virus, Trojan, or system command access seems consistent now with our viewing the behavior of a Cylon virus on Galactica in "Flight of the Phoenix", although the CNP was never loaded on their computers.
It's reasonable to assume that post-war (modern) Colonial ships were still not easily hackable despite their advancements, so it took the CNP backdoors to make that happen. As far as Galactica was concerned, it's relatively primitive computers were not as advanced as those used on other Battlestars and were more likely to be directly infected, as done in "Scattered""--IF they were accessible by wireless. Obviously the computers were never available for infection until the events of "Scattered".
It's likely that the process of networking Galactica's computers with hard lines at Gaeta's console (Gaeta mentions in "Scattered" that he would network the FTL computer with the Navigation, Damage Control, and Fire Control computers) also interfaced them to the comm channels of the ship and to ship's wireless by default. Otherwise, Gaeta would not be fearful of simply creating a closed network to make the calculations. Networking any computers on Galactica would automatically create a wireless portal to them. Interesting Colonial technology in that way; it's like two laptops that automatically form a wireless connection when they want to share data.
So the Raider's programming may be two-fold. Option one: Attempt access to an enemy ship via a CNP backdoor, where it may activate a Trojan Horse program in the CNP or directly command the CNP to stop operation of the ship. Option two: Use First War tactics and attempt to hack and infect a computer that's available by wireless. Just my take on it, but it's consistent with show events. Spencerian 15:46, 23 September 2005 (EDT)