The first thing I'll say is make sure not to conflate deep web and dark web (as that wikipedia article you quotes also says). They're different concepts, and it's not all necessary a bad thing- it (deep web) basically can refer to any non-indexable part of the internet, and while an obvious use of that is for criminal activity, there are perfectly legitimate reasons for a page or part of the internet to not show up on google search results- I don't want my bank account or email pages turning up if someone googles me, for example. That's all 'deep' web, and that's part of why that 96% statistic exists. The dark web is a
subset of that, in that it's also unindexable, but it's far from the majority. Most of that 96% is just stuff like the emails and bank accounts and whatnot that have obvious but not malicious reasons for being 'hidden.'
The dark web tends to be the more nefarious stuff, although again, not everything on the "dark web" is necessarily bad, either (like your OP says, in some cases it's used as a way to distribute information in places with strict controls on the press, which is a very
good thing, or for other kinds of whistleblowers). It's not really something you can just stumble upon, by design and definition- you pretty much ahve to be specifically trying to access it. Some of it is also just ideological opposition to what they would see as an "overregulated internet," or just hobbyists doing random crap through certain connectivity protocols, much like the internet itself. This is why saying things like "police know about the dakrnet but don't shut it down" isn't really a meaningful statement- yes, crime exists there, but it's sort of defined into this space, in the same way that you could just say crime is on the internet but they don't shut it down. The Deep Web is a (sizeable) subset of the internet, and the dark web/darknet is a very small subset of that, and the illegal activity that happens there is also an even smaller subset within that.
To address this more specifically:
3. The U.S government knows that the deep web exist, but doesn't stop a lot of illegal activity on it.
It's one thing to say you're aware of the content existing, but the specifics get more complicated. Knowing how to track it to find those responsible and rooting it all out isn't a simple matter of flipping a switch to shut off the whole dark net, it's just a term for a specific subset of computer networks. For one thing, while governments can be aware of it, typically the users would be fairly good at hiding themselves (which is how it occurs in the first place), and they have to be able to act on that information. The US government, for example, only has jurisdiction
in the United States. Like any criminal organization (for lack of a better word/as an analogy, we'll treat the criminal subsets/networks like a bit of organized crime), you can know they're there, but not know who's involved or how deep it goes. If you happen to catch one part of it, or one member, sometimes infiltration and monitoring instead of directly stepping in to shut it all down at once can be the best way to effect the most change or stop the most crime. If there's 600 people doing something, but you make yourself known by grabbing one guy or shutting it down, that whole infrastructure just reforms somewhere else. There was actually a recent raid on a child porn ring from it.