Right now, in the real world:
Just about
EVERY major function of life and government is online.
Railway/subway/transit lines
Electrical power grid
Traffic lights in major cities
EMS
Police services
Various Social policies
Medical charts
Banking
Telecomms
that is NOW.... not in the dystopic cyber future

And, just like in SR... These systems can and do come under cyber-attack, and do get breached. You just don't hear of it, because well, the media can't figure out a way to blame Trump.... (there are Riots in 6 countries, Wars in 4 more, social unrest in a dozen more, disease outbreaks in 8 more.... yet Google News is full of Trump Twatter crap....)
Now, the history of computers, the matrix and all the crap that goes with it is a lot different in SR, then our world... but you can see the inspirations, and why they needed to update to a "wireless" system. (after all, why is the game that is set in the future, needs its "internet" to be wired, when the players are looking shit up wireless?)
Now when you get right down to the basic set up of the matrix, its not that
bad really... in a thematic sense... (in a rules sense.. it get wonkty. Don't have 6e yet so no comment on it ATM). The Matrix is made up of millions of interconnected devices to share both the bandwith and processing power required to run all the activity. (so, even when your commlink is not being used by you, its STILL acting as a "pass through" device for everyone around you).
And this works and is
SAFE because the devices sold to the public can not
change the data they access, and the device that can change the data are limited to the corporations (and those that steal the tech - like runners and the black market)...
Keep in mind: There is are BILLIONS of people in SR, yet only a thousand that actually have the equipment and talent outside of the corps to actually "hack" matrix.... (and the technomancer population.. which is just one MAJOR reason why the Corps fear them)... Which is another reason why the entire system "just works".... to steal a catch phrase (and all its intended meaning

) The number of actual threats are so low.
As for security systems...
well... They will be as advanced or as little as the company feels is warranted (Same as today). And just like today, the more advanced ones will be connected to the matrix as the corp dictates. So smashing into the Azzie owned Stuffer Shack probably isn't going to trigger more then an alarm and alert to local Police. But the Azzie Pyramid in Seattle? When an alarm is tripped there.. Azzie SA, Azzie EU gets alerted along with every other Azzie asset in Seattle!
Why?
Because Aztech doesn't care about the Stuffer Shack or the employees there. But they care very much about their North American Headquarters!