This is nothing to do with node. This is poor programmer decision making. You can build great node apps with a real minimalist approach. Holding up projects which pull in half of npm as "the world of node" is like holding up a hot and ready 5$ pizza and saying all Italian food is bad.
Most other ecosystems inlcude more batteries (e.g. PHP). That is why you have to update this ecosystems with all their modules.
The problem is, if the core has a bug, ALL apps in this ecosystem has the bugs.
node includes not everything and concentrate on the core. If modules have bugs, not all apps a compromised.
It is a fundamental design decision, if you not like it, don't use node.
You can include all dependencies manually and update them manually, nobody keeps you away. But have fun to update all your deps.
Encouraged by who? I see the same people which used to install jQuery or WordPress plugins and were able to get janky but working sites. But prolific module authors and node core contributors don't promote these approaches.
Maybe if you listen too much to twitter "thought leaders" you might get this impression, but we are all aware of the problems with social media platforms...