The part you quoted says that those parts of the agreement do not terminate. But the “Your Content” section of the agreement says:
When Your Content is removed from the Website or the Public Registry, whether by you or npm, npm’s special license ends when the last copy disappears from npm’s backups, caches, and other systems. Other licenses, such as open source licenses, may continue after Your Content is removed. Those licenses may give others, or npm itself, the right to share Your Content with npm Services again.
The “special license” indeed terminates. The part that doesn’t terminate is npm’s ability to use any open source licenses to continue sharing the code.