The problem here is orthogonal to bundling, unless I've missed something in the discussion. You can have a Node/NPM-style package manager without doing bundling, and you can bundle together a Deno project if you wanted.

Bundling is mainly a front-end technique used for performance reasons - you don't want to resolve and load each import separately, so you combine all the files into a single one for the sake of efficiency. But for server-side Javascript - be that NodeJS or Demo - you typically don't need to bundle anything because resolving files doesn't take a slow network call.