Yes, versions aren't usually pinned at the package-level, so if you install a new dependency that introduces the trojan to the project, then yeah your are compromised. Not sure if that happens to "millions of servers" in a few weeks tho, it'd have to be a pretty popular package at least and remain undetected when these millions of developers presumably test the new code that their new dependencies introduce.
Having versions tightly pinned in the package-level isn't a free gift. It'll lead in lots of duplicated versions of a practically same package being installed and ran when two higher level dependencies have a transitive dependency to sligthly different (but in practice compatible) versions of the same package.
Edit: I agree with the points about sandboxing and permission configuration, etc, though. That's hopefully also coming to Node at some point.