2 - personally I don't see why you'd want to use anything other than Typescript right now. It certainly feels like TypeScript has "won" and is now the defacto standard for anyone doing any kind of work in the JS-ecosystem. That of course may change in the future of course, but today it feels like TS is where its at.
3 - I've experienced a lot of annoyance shipping around huge node_modules/ directories, just to get a CLI app working. Sure these are not "problems", but it is a pain to have to compress up hundreds of thousands of files and then decompress again rather than just moving around one executable.
4 - deno is the "package manager", if you can call it that. You explicitly state the imports & versions you need in your code as import statements, and the deno runtiem handles sourcing the files for you transparently. So either from a cache, or at first run it will try and go out onto the network (internet or proxied IIRC) to get them for you.