I haven't used one of those yet, but I'd think that private npm registries are an option to safeguard yourself against losing dependencies. Like Claudio below said: The issue showed everyone that there is a risk to the "make everything a package" approach. Now we know it, we'll watch out for it, put mitigations in place, and move on.
Modularity as a code design idea is still immensely advantageous (readability, testability, scalability, velocity of deployment etc etc). It's just not perfect and needs caution.