And security updates, as you said, are needed regardless of whether you run Docker on top. I think Docker is a needless complexity and security risk.
I see two main places where Docker provides a lot of value: in a large corp where you have massive numbers of developers running diverse services on shared infrastructure, and in a tiny org where you don't have anyone who is responsible for maintaining your infrastructure full time. The former benefits from a standardized deployment unit that works easily with any language/stack. The latter benefits from being able to piggy-back off a cloud provider that handles the physical and OS infrastructure for you.
Relying on hidden complexity makes for a hard path ahead. You become bound by Docker's decisions to change in the future.
For example, SSLPing's reliance on a lot of complex software (among which NodeJS and Docker) got it to close, and it got on the front page of HN recently.
https://news.ycombinator.com/item?id=30985514
Keeping dependencies to a minimum will extend the useful lifespan of your software.
(Has it occurred to you that it losing money for a while might have contributed to its eventual unmaintainability, as the dev opted sensibly to work on more sustainably remunerative projects? If so, why ignore it? If not, why not?)
Similarly for the Node aspect - that's very much a corner use case related to this specific application (normally SSLv3 support is something you actively don't want!), and not something that can fairly be generalized into an indictment of Node overall. Not that it's a surprise to see anyone unjustly indict Node on the basis of an unsupportable generalization from a corner case! But that it's unsurprising constitutes no excuse.
Other than that you seem here to rely on truisms, with no apparent effort to demonstrate how they apply in the context of the argument at which you gesture. And even the truisms are misapplied! Avoiding dependencies for the sake of avoiding dependencies produces unmaintainable software because you and your team are responsible for every aspect of everything, and that can work for a team of Adderall-chomping geniuses, but also only works for a team of Adderall-chomping geniuses. Good for you if you can arrange that, but it's quite absurd to imagine that generalizes or scales.