Dependencies are a two edges sword. It's good that you get security updates. But if you can't review all the changes, security issues can also sneak in. Like if someones npm account get hacked and the hacker sneaks in a remote shell or backdoor. Those can be hard to find if you got millions of dependencies which get tons of updates every day. So I usually lock down dependencies, and NPM becomes a fancy tool for copy/pasting.
This duplication is necessary because npm is not a curated software distribution designed to work as a cohesive system. Anyone can push software to npm. As a result, there are packages that depend on different versions of the same library and they must have their own individual copies of the dependency in order to work. This isn't the case in a Linux distribution with maintainers: there's one instance of the package that's shared by all other packages.