Clarification - my point was that a sane person prefers dependencies to be explicit and manageable. It is easier to create tools for that with static languages. As for NPM due to dynamic nature of JS the tooling is rather hard and just not there yet.
Dependencies (and their specific versions) are already managed explicitly via package.json.
The shift to a flat dependency hierarchy in NPMv3 will make managing dependencies of dependencies much more explicit and straightforward to manage.
JSPM already uses a flat structure and shows how simple dependency management can be.
I'm not sure what you mean by "the dynamic nature of the tooling". The JS development ecosystem doesn't attempt to provide an end-all-be-all monolithic core lib. It's a good thing and one of the primary reasons why advances in the JS evosystem are happening at breakneck pace.
