You would hope a new module would reuse as much previous base modules as they can, but sometimes it's enough to just put some new code in that namespace, with the intent then that someone will find it easier, and build off of it. The hierarchy is for organization, discovery and distribution, as much as it is about good software development practice. The goal being to improve the overall software development ecosystem.
(and I was a professional Perl programmer for the first 5 years of my career, so I'm not asserting this out of lack of familiarity with CPAN!)
That all said: I don't even think what you're saying about CPAN is terribly similar to the situation being discussed here, since Go's x/crypto/ssh (and all other x/ packages) are officially part of the Go Project and are maintained by the Go core maintainers. See https://pkg.go.dev/golang.org/x. Third-party Go developers cannot add new packages to this namespace at all.
I originally created my knownhosts wrapper to solve the problem of populating the list of host key algorithms based on the knownhosts content. Go's x/crypto/ssh provides no straightforward way to do this, as it keeps its host lookup logic largely internal, with no exported host lookup methods or interfaces. I had to find a slightly hacky and very counter-intuitive approach to get x/crypto/ssh to return that information without re-implementing it.
And to be clear, re-implementing core logic in x/crypto/ssh is very undesirable because this is security-related code.