I think I found the problem, our code in cmd.go:InternalToolPath() assumes that there is always a /snap/core/current symlink. However that is not the case when we refresh core for example.
This PR: https://github.com/snapcore/snapd/pull/3512 should fix it. It simply takes filepath.Dir(os.ReadLink("/proc/self/exec")) as the base-dir for the InternalTools (like snap-seccomp or snap-update-ns).