Yeah I understand being uncertain on how to proceed with computers and virtual matrix situations. These really isn't much guidance in these things. I've looked it up and we have a really good framework and description of the network. I'm reading the SYNC, PANTHEON, PANT-IES, Nodes, Network, etc. We don't have a story precedent on how it works outside of star ship operations. Since this is a star ship based RP I can't find much about hacker wars. It all reads like a really powerful, stable, and highly connected futuristic internet. Unfortunately, just like today, the bigger the system, the harder it is to defend everything.
Long exposition short, for the sake of application to the story, I think at best Celine would only be able to offer maybe a +2 Luck buff to the crew, maybe an extra saving throw. She doesn't have to know everything nor would she really change or be able to affect the fish bowl mentality. The more she tries to interact with the greater the chance of detection. If she wants to be able to affect devices (whatever it may be) she'll want to keep her interaction to a minimum. Especially if she's not there looking to dig up military secrets or act as a hostile entity.
Long exposition long, no system is perfect. From what I've read and from the direction I'm seeing just modern day technology going, the dangers of interconnected systems are just as severe here as they are today. There are tons of ways for someone to find a back door or less guarded access point. Even if you guarded everything, some things would need to connect with others and to restrict it removes it's ability to function. As for how its possible to hack just about anything, from everything I've read, the system is very interwoven. It's like super universal wi-fi. If we want things to work how they do, it would be needed so wires are no longer as much of an issue except where isolation is needed.
You know what, I found a better way to explain things. From my time working with security, I can say a lot of this is pretty legit and the guy on Game Theory does his homework. And yeah, I understand Watch_Dogs is..... contrived and we don't have convenient high pressure pipes and devices everywhere. No guarantee the links work. >_>