That's true. However:
Every dependency you add to your project is also a commitment.
When you add a dependency, you're committing to deal with the fallout if the library you're pulling in gets stale, or gets taken over by an incompetent dev, or conflicts with something else you're using, or just plain disappears. If you add a dependency for just a few lines of code, you're making a way bigger commitment than if you'd just copy/pasted the code and maintained it yourself. That's why so many people are shaking our heads at a 17-line dependency. It's way more risk than it's worth. If you need a better stdlib for your language (some of us write PHP and feel your pain) then find one library that fills in the gaps and use that.
This is a problem with NPM, not with dependencies. With different package management systems with stable builds and lockfiles, then you pin to a specific version and there is no way upstream can cause problems. A lockfile is a pure win over vendoring.
The only way to prevent this is to have your own local server for third party package repository.
For example, I was a maintainer for an admin UI component of the last version of Drupal core, and we decided to pull in a query string handling library written by Ben Alman. It was a good decision, and it hasn't caused any problems. But it still meant we were trusting him to maintain part of our codebase. It was also an implicit commitment to every user of Drupal that if Ben quit maintaining that library, we would step in and fix any problems that came up. You don't get rid of that commitment with a lockfile.
Actually that's not correct when using node/npm (or anything else in the ecosystem like browserify). That is one of the impressive things about this platform: any number of different versions of the same module can be required by the same app. It would be nuts to do that in your own code, but as long as the craziness is in your dependencies it really doesn't matter.
If there is a security fix, you should bump your dependency by hand, the other problems that you pointed out do not exist in Node (and it's about time they disappear in Java)
If its just a few lines of code, just copy the thing into your code base? throw a comment in saying "came from xxxx" so anyone reading your code knows that it might look like a overly generic function because it is.
Honestly, and this is maybe just me being biased against JavaScript, then this is what happens when you pick a language fully knowing it's limited in all sort of silly ways and attempt to use it as a general purpose language. It's not that you can't, but if you need say typing that can tell you if something is an array, then maybe picking JavaScript to begin with wasn't the brightest idea.
There's a ton of libraries and hacks out there, all attempting to fix the fact that JavaScript isn't really good general purpose language. ES6 is fixing a lot of these thing, but it's a little late in the game.