Yeah, I updated my comment to reflect that, you definitely would only need versions of functions on disk where some code depends on it. That's basically how container layers work.
I think CI/CD practices are really important to get rid of the old code. Automated build systems should be constantly downloading new versions of deps and running tests so devs can fix bugs quickly and release new versions that depend on new deps. The quicker that cycle happens, the quicker old code can disappear, new functionality can be implemented, bugs can be fixed, etc. Because everything would still use pinned versions of deps, it would still work exactly as it was tested, so you wouldn't be sacrificing reliability for up-to-date-ness. Speed and automation of that process are critical.
I think CI/CD practices are really important to get rid of the old code. Automated build systems should be constantly downloading new versions of deps and running tests so devs can fix bugs quickly and release new versions that depend on new deps. The quicker that cycle happens, the quicker old code can disappear, new functionality can be implemented, bugs can be fixed, etc. Because everything would still use pinned versions of deps, it would still work exactly as it was tested, so you wouldn't be sacrificing reliability for up-to-date-ness. Speed and automation of that process are critical.