I have installed many debuginfo RPMs, but fedora-debuginfo is disabled in /etc/yum.repos.d/fedora.repo. I ran an update with gpk-update-viewer, and only packages in enabled repositories were installed. Immediately thereafter, I ran an update with yum, and all the corresponding debuginfo updates were installed, reportedly from the disabled fedora-debuginfo repository. I would not expect applications to install without warning updates from repositories that are explicitly disabled. For example, I installed packages from updates-testing, but I have intentionally disabled it to prevent my system from being destabilized by relatively untested changes. It is nice that yum notices that updates to these packages are available and probably needed to match the updated binary packages, but I think the user should at least be explicitly warned that packages from disabled repositories are about to be installed. I would also expect the behavior to be consistent between yum and gpk-update-viewer. gnome-packagekit-2.31.91-2.fc14.x86_64 yum-3.2.28-4.fc14.noarch
I suspect you have the auto-update-debuginfo plugin enabled in yum. If so, you'll see that is explicitly what that plugin does: enable debuginfo repos to get updates for debuginfo pkgs you may have installed.
Also note that the reason PackageKit doesn't update the debuginfo rpms is because it explicitly force disables the auto-update-debuginfo plugin. You'll have to log a BZ against PK if you want that fixed. Or use yumex.