First off, a bit of history (seriously, I started a Q&A thread about the world because I LOVE the history of this game). When the Matrix crashed in December (of course) 2064, a new wireless Matrix was implemented. It's a lot closer to what current cell phone technology is than wifi internet today, in that's it's broad-spectrum and is pretty much everywhere. There was a MASSIVE shift to cloud computing, which is why no one worries about stuff like storage anymore. Pretty much everything was connected to this new Matrix because the hardware to run it was very expensive (I think the server I bought for my decker in 4A cost me like 300,000¥ and it's a small one). It took more money than a starting character can even get in the game in order for me to be able to pull all my household appliances and everything else off the grid.
In Storm Front (the transition eventbook that shifted SR4 to SR5), the Corporate Court through their Grid Overwatch Division (aka GOD) implemented sweeping new security protocols that locked everything down. In the book, you can see it took months for even legendary deckers like Fastjack to crack the new protocol and it involved breadboxing hardware onto his commlink (thus why we not have commlinks and cyberdecks both in this edition).
Now, commlinks are still pretty necessary for all characters. It stores your ID and your money. In some places like Manhattan, you can be arrested if you don't have a commlink with a PAN broadcasting your SIN. Legitimate users basically use their commlinks as the central unit to manage all their gadgets (and EVERYTHING is a gadget in Shadowrun). Because of this, pretty much all your gear is slaved through your commlink which has a direct connection to your brain for mental commands, either through a datajack or through trodes (more common). Because of this link and the subroutines involved, you're able to perform actions a lot faster through your commlink than you would manually.
Here's the thing...there is no "direct input" for most things unless you mean some sort of manual activation. The commands have to come from somewhere, and that's through your commlink. Unless your stealth armor is directly plugged into your brain (which technically is possible but would look just silly), there's no real way to tell it to change from urban to forest camo when you hop the fence into the park. Those commands come from your commlink, which is why they have to be wirelessly enabled for you to access them on the fly.
For example, the forearm snap blades you mentioned before. In previous editions of the game as well as this edition, the blades are extended or retracted manually through a muscle command - basically, you flex your forearm muscles in a certain way and the blades pop out. Or, if they're wirelessly enabled, you simply think "Blades out" and the blades pop out. It's faster and it doesn't distract you from doing something else with that hand.
The laser sight goes more into what exactly AR is. Augmented Reality is an overlay on your own vision via Image Link cyberware (included with all cybereyes), glasses, or contacts. It displays information as you walk down the street, from advertisements for the sale going on at Stuffer Shack to the single's profile of the girl walking past. This is useful for mundane purposes, but most of the mechanics in Shadowrun revolve around AR's uses in combat. A smartlink, for example, transmits a ton of data about the gun to you - how many rounds you have left, the range to the target you're aiming at, etc. Laser sights do something similar but with less actual information when that data is routed through your commlinks processor - it determines range, it tells you whether the portion of the person you're targeting is protected by armor, stuff like that. It's not as good as a smartlink's detailed info, but it's enough to give you a slight edge in a fight.
The oddball out of your examples is the silencer because at least they tried to explain the wireless bonus on that one. I mean they really tried. It's just a hard concept to get across in two sentences that also include the rules mechanics. It basically works the same way active noise reduction headphones work today. You can mostly cancel out a soundwave by producing another soundwave that specifically mirrors the first one. It's not perfect, but it helps a lot in reducing sounds. And that's what the silencer does - it has a microphone and a speaker on it and, when the gun is fired, the microphone sends the sound to your commlink which analyzes the wave and commands the microphone to produce a countering soundwave, thus further reducing the sound the gun creates. Without the wireless connection to the commlink, there's no processing power available to analyze the soundwave so a counter-wave can't be produced.
I can clarify more if it's still murky or if there are other bonuses that don't make sense. Again, this is a problem with the book trying to cram so much in. The book should have thoroughly explained these concepts as they relate to the game rather than presenting the world as it is and leaving it to you to extrapolate how a lot of this technology works.
