Yep, but that was because SR has basically painted itself into a corner with it.
In play Cryptoanalysis trumps any cryptography. No matter what level of coding you used, all you needed was a single extended test based around a CT and you were in.
Now there were gaming reasons for this, the classic go get pizza scenario tends to occur otherwise, but the end result is there are few real ways to secure your tech from being permanently usurped.
But that is why the master nanohive for these should be an offline design and the nanites built to be non-reprogrammable. They can only do the task they were built with and the hive makes new ones to fit new tasks. By itself it should be able to maintain a high enough pool to fend off initial attempts by outside nanites and not let them get a foothold to start with.
But that doesn't work out so well because CFD is the miracle hacker... could hack/hijack both hard and soft nanites, even those built to be non-reprogrammable, infecting equipment and people alike, PLUS it seemed to shrug off several treatments that normally should have worked against them, won't even go into that rant.
Again this was done for game reasons, otherwise players would have yawned and debugged themselves and loved ones with minimal effort.
But at the end of the day, in their attempt to create a new boogeyman they created a September Monster which has quickly become a take it or leave it option to the game that many tables just ignore because it just doesn't mesh well with their campaigns.
The funniest part is they sort of have been down this path before with Ghouls, what with the contact infection vector, which created the possibility of someone just grinding a ghoul or two and feeding it into a city's water supply or Stuffer shack snack rack to infect a city. They eventually changed that infection vector, but really what did they think was going to happen with CFD?
But on a lighter note, if you want a more humorous view of something similar, check out High Aztech by Ernest Hogan. Where they create a religion virus (can substitute soft nanites here basically and passable by skin contact) that reprograms the victim to believe in a particular diety or set of dieties, even having hallucinations about interacting with them. Originally designed to infect the local populace with a passion for the traditional Aztec pantheon, it quickly gets messy as every major religion unleashes their own version. But the twist here is rather than one set of deities overriding the other, the brain of the victim starts to intergrate the multiple gods together so now you have Buddha hanging out with Quetzalcoatl partying with Loki inside their head, making for some humorous insights.