The conventions and resolution approaches that are needed to accomplish this often end up being opaque, less flexible, and harder to work with.
I much prefer the approach of C, C++, and even PHP to some extent, where the interaction with the filesystem isn't hidden.
When using C or C++, it's trivial to reference a globally-installed library, such as the standard libraries of such languages. It's also simple to reference third-party libraries, or even to include local copies of third-party libraries within one's own source tree. Relative or even absolute paths can easily be specified when referencing external code.
This also gives so much more flexibility with regards to how a project is laid out, and how it pulls in other code or libraries it depends on. I can follow an approach that works for me, for my project, for my team, for my version control system, for my development environment, for my deployment environment, and so on.
I want the language to conform to my needs. I don't want to have to modify my behavior and my environments to conform with what the language's developers deem to be the "right way" of doing things, especially when this isn't compatible with my needs.
Maybe this means there's slightly less consistency with how libraries and dependencies are handled across projects and libraries, but that's a cost that I'm willing to pay, and in practice it actually isn't that much of an issue when using languages like C and C++.
I'd much rather spend a few seconds specifying "-I" and "-L" and "-l" options when compiling or linking than trying to remember a bunch of conventions or how the high level package names end up mapping to the installed modules or libraries.
I'm not saying that the C approach is perfect, or that I'd want other languages to use a C preprocessor like approach of actually combining separate source files just prior to compilation or even execution.
But I would really like it if modern languages didn't try to hide the existence of files and directories so much, and didn't try to force conventions on me. I'd rather deal with the very small cost of explicitly telling the compiler where to find dependencies rather than relying on conventions or opaque resolution processes.