As @Ghanima pointed out,
apt-get doesn't have the ability to know about every file that's installed on the system. Most files that are put under the user directory (
/home/pi in this case), are done after the installation process.
There's good reason for this. Let's say you install a package called foo, and your only user on the system is pi.
apt-get installs foo, and then puts the appropriate configuration files in the
Later down the road, you add another user called "cake". Since cake wasn't present when the installation process occurred, that user doesn't have any configuration files within their profile. Your new user tries to run foo, and it promptly crashes and dies.
You could fix the crash by having foo write the config if it doesn't find it, but again, we're back to
apt-get not recognizing that there is a file sitting under
/home/cake. It wouldn't make sense for
apt-get to remove some of the user configurations and not others. In fact, it may give an admin an illusion of success when they really shouldn't.
It happens in Windows too:
This isn't limited to
apt-get. When you uninstall something in Windows, you rarely remove the files under
%userprofile%\AppData. Some uninstallers will give you that choice, but again, it's not usually a default. I'm not even going to go into detail that is the nightmare known as the Windows Registry...
It probably happens in Arch too:
I have extremely limited experience with Arch, and by extension Pacman. I can't say with any authority that it has the same problems, but I would logically assume that it does. Unless they're putting in an unrealistically huge amount of work, there's no reason why it wouldn't.
It's not a big deal:
I am concerned that overtime my system will have a lot of useless junk that apt-get did not keep catch when uninstalling the program.
And what problem does the useless junk really entail? Configuration files are tiny, little things. Many are measured in bytes, and few are more than a couple KB. It might be annoying from a general principle kind of thing, but unless you're installing and uninstalling a huge amount of applications (that presents other issues) it's just not going to cause any kind of system issues.