You're not going through their brain - you're piggybacking on whatever establishes the DNI. DNI isn't your brain, it's an interface between your brain and various devices. Hence why the DNI must be established by some particular piece of hardware.
I think that taking a step back and looking at the definitions might be helpful here: DNI = Direct
Neural Interface. Cyberlimbs are an extension of modern day prosthetics, their
neural interface connects to the nerves that used to connect to the limb. Yes, there are other cyberware that's implanted and has DNI, with the vast majority of all cyberware having DNI, but that's a component of each implanted cyberware and not a centralized system. I think you're making an erroneous presumption that all cyberware is connected to each other - they're likely all connected to the PAN, but not likely to each other.
You do, however, require an implanted commlink, datajack, implanted sim module, or trodes to establish a DNI - see the definition on page 217, SR4A. There's also some sections of Unwired that you should take a look at, such as page 102; it establishes that the DNI is a way for a hacker to gain access to cyberware.
The target character may be shut out of controlling his own
implants by deactivating DNI or altering the account privileges
(requiring a Hacking + Editing Test).
This is the closest thing that I can find to your mention of DNI being a way for a hacker to gain access to cyberware, and it's not. It's a hacker
shutting off access to cyberware. DNI is normally a means to
prevent a hacker from getting into your 'ware, and it stops this generally by removing the wireless, not adding a new means of an outside hacker communicating with your implants. Unless you're saying that the hacker slaps on some double-sided trodes and goes into grappling with the target, in which case he deserves to have his neck snapped for trying to hack while in melee with a sam.
I'm inclined to assume the implantation of your first DNI-enabled ware includes the implantation of the sim module.
I'm curious where the idea that DNI includes a Sim Module comes from. There's no need for special firmware conversions that facilitate VR when you're attaching a cyberhand that lets you resume use of a hand that you previously had, used conventional nerves to control, and then go back to using nerves to control. Cybered characters don't need to rig themselves just to use their 'ware.
just like how you can "click" and interact with AROs with image linked glasses alone.
Those glasses need to have wireless enabled in order to receive the AROs, and the book mentions devices like AR gloves or keyboards or such that are needed to control and interact with AR. I'm sure there's an eyeblink system that allows similar functionality, but it's not the standard presumed in SR4.
a device with both wireless and skinlinked functionality, but that's clearly a bad idea. It sounds unlikely to me, but I'm mainly being cautious.
Devices with skinlink can be set to default to skinlink, in essence shutting off their wireless - this setting would then toggle back to 'wireless on' if your skinlink is ever broken, such as if you have a smartlinked gun and it's knocked from your hands.
I'm pretty sure you can actually have really short-range transmitter (like 10 cm range) in a glove
Signal rating 0 is roughly 3 meters. Either way, I think you're right that skinlink isn't perfect (though it probably wouldn't be disrupted by sweat - look up galvanic skin response, a technique in some psychology experiments to measure physiological state), and the military would likely have more of a reliance on tried-and-proven wired.
Your better off running them both through a skinlinked comm, so that you can get other benefits of AR.
If they're both linked to a skinlinked commlink, which is a wireless device, they're now (indirectly) connected to the outside wireless world. Unless you're talking about operating two commlinks at once, which is something I've done on several characters before, but you still need to have the image link connected to something wireless or you can't interact with AR.
Though, a question occurs to me: given that a cybersafety then has to get input from somewhere, does that mean the safety could, in theory, be hacked?
In theory yes, but the cybersafety in Shadowrun is based on a wireless security chip that exists NOW, and has a signal range of something like 5-10 centimeters. One's implanted in the gun and locks the gun's safety mechanism if it's not in range of the safety chip, which is usually in a wristband or such easily worn item (or an implanted chip in Augment).