I guess what I'm asking is what is the typical matrix security setup of an average non-retail office? One that has no reason to make themselves accessible outside of the building (since work is all done by employees in house).
There would be a host for the building, though the host might be rented cloud space. The host would manage (at a minimum) the security systems, access logs, archival, and probably employee programs (since you wouldn't want any data being stored on the employee's commlink or whatnot). There have been numerous references in the fiction of terminals still existing, though we have no rules for terminals. Assume that the employees come in to work using their commlinks for identification purposes. They would maybe have physical keycards, biometric locks, or combination pads to access the more secure parts of the building. These would, of course, be the parts the shadowrunners want to get into. Once the employee is in the building, their presence is logged and tracked as they go to their terminal to begin work. The employee most likely works in AR for normal work, but might pop into VR with trodes or a datajack for more intense stuff, like collaborative programming and research simulations. At the end of the employee's shift, probably 10-12 hours, the employee leaves the way they came in.
From the outside, the building would have a host (probably silent, but maybe not if they're expecting visitors like delivery people). The commlinks of the employees would be visible, though the building might use wifi-negating paint to block the signals for security reasons. Any devices in and around the building, like security cameras and access points (maglocks, etc.) would definitely be running silently. The device is probably slaved to the host, but might not be if it's easily accessible. Any device that can be connected to physically is a back door into the host, so expect any devices that are slaved and accessible to be using motion detectors on their cases at the minimum.
Some security devices are passive and don't necessarily require access to the host in order to function. Examples would be pressure plates and induction pads (typically found in grassy areas). A great security setup will minimize access points, maximize visibility, and attempt to funnel a would-be intruder to a pre-determined location. For instance, you might put up a bunch of bushes that hide monowire. If the intruder notices the monowire, they skirt around the bushes. But the only access points between the bushes have induction material to detect weight and the body's electromagnetic field. All of these devices are passive, meaning they really don't need to be online at all and won't have any kind of matrix presence.