As soon as you take 2 dependencies in any language, there's a chance you will not be able to upgrade both of them to latest versions because somewhere in the two dependency subgraphs there is a conflict. There's no magic to avoid this, though tooling can help find potentially working versions (at least by declaration). It's often the case that you don't encounter conflicts in Python or other languages, but I don't imagine that Go is immune.
I've used npm but an not familiar with these kinds of details of it. There would seem to be some potential putfalls, such as two libraries accessing a single system resource (a config file, a system socket, etc.). I will take a look into this though. Thanks.
npm works around some problems like this with a concept of "peer dependencies" which are dependencies that can only be depended on once. The typical dependency, though, is scoped to the package that requires it.
Rust can include different versions of the same library (crate) in a single project just fine. As long as those are private dependencies, no conflicts would happen. A conflict would happen only if two libraries pass around values of a shared type, but each wanted a different version of the crate that defines the type.