Apologies for hitting this old topic, but unfortunately can't stop myself.
The Matrix being hackable in this way seems to me to be based on two things. One - narrative and having a game to play (basically the game equivalent of the anthropic principle), and two - an extension of the real world approach to security.
We live in a world where it has become apparent that it was more important to our security services that they be able to hack our systems than that our systems be secure, and they had sufficient influence to dictate that to tech corporations. I disagree with that view of security, and believe that security services should protect their citizens by improving our security, but they do not seem to believe that. They were involved in the standards bodies that determined which security standards were agreed. Did they push those bodies towards standards they could hack? I don't know for sure, but I have spoken to a member of those bodies who believed they did. They have certainly campaigned behind the scenes for back doors into systems that could then also be used by other parties. They have intentionally reduced our security in order to make it easier to spy on us.
Now, personally I'm hopeful that the power of real world corporations will kill this off, they are moving in this direction, and if this doesn't happen, countries where it does happen will probably end up hosting corporations who will end up the dominant tech companies. The really lucky countries will be those where the security services decide their aim will now be to protect their citizens rather than their governments.
The Shadowrun world does not have to have gone that way (and nor does ours). A world in which any hardware/software manufacturer might desire the ability to brick your device is a world in which a hacker can do so (sure, if the key to that backdoor were known only to one person, the code for it somehow embedded in a chip, all designs for it destroyed, and somehow the chip unreplacable,, etc it;d be close to impossible, but that's unlikely).
My (naïve) view on the matrix of SR5, having not played other versions, in as far as it makes sense without magic (I do find the posts suggesting magical involvement persuasive) is that the way the matrix works is that we have stupidly huge numbers of low power (by SR5 standards) devices, in a mesh wireless network. sharing processing. As such you gain wireless bonuses from having this shared processing. You have 'noise' when there aren't enough devices to mesh with or share processing with for the tasks (static zone), as well as when things are too busy for you to get enough local devices to mesh with or share processing with (spam zone). I find it very possible to believe that a brute force attack can damage a device, considering that perfect security for the owner is very unlikely to be a design goal (especially for things that could be used to hack a corporation - why make them immune from your IC), but it could even work by altering the shared processing in other devices in order to change the code, if it could work out what the shared code was doing.
However, gameplay trumps realism anyhow !
