I'm not comparing single-file vs multiple files, I'm comparing single-file vs NPM/PIP/go get/Cargo
Let's say you depend on foo, which depends on 10 other libraries including bar, all of which depend on a library called baz. Then one day someone discovers an exploit for baz.
With npm, you only have one version of baz installed, and can easily check if it's a vulnerable version.
With single-file libraries, baz was built into a single file. Then bar was built into a single file containing baz. Then foo was built into a single file containing bar and other libraries, all which included baz.
Now your library contains baz 10 times, all of which might be at different versions, and none of which you can easily check. (You can check your version of foo easily enough, but baz is the library with the exploit)