Why would using pypi/npm/crates be better? If I'm already using git (which I will be) then using something else for package management needs to be a huge step up, especially if the other systems you mentioned are language specific and a git solution would probably be language agnostic.
My assumption here is that your language has already got a dependency management system beyond git, because there's just SO much value in specifying and isolating dependencies and associated build tools, things git doesn't care about (off scope).
Just a few off the top of my head: identifying/resolving transitive dependencies and conflicts, separating development-only deps, optional dependencies for extra features, dependency ranges for pinning and exact locking, proxying/caching for offline-ish rebuild, auto-upgrades, license checking (GPL...), CVE flagging... All these are ~standardized per language.
If you've got (say) a Python script in git, and submodules seem like a good idea for specifying all your dependencies, instead of going towards a package manager, it feels to me like we're a long way away from sound, practical engineering.
For language agnostic, I'm sure the Nix/Guix folks can hook you up with a variant of this, even while using git (maybe even submodules!), but all the value I specified above is still there.
I guess I don't mind git, maybe even using submodules, but I hate the substitution of good package management hygiene over "just import the next folder down, which I submoduled now".
