Why are apk files are kept in system folder? Isn't an apk files just an archive which is unpacked when you install a package? So, why should it be kept then?
APK files aren't unpacked when you install the app. The APK file is the only copy of the executable code and static assets belonging to the app. Deleting the APK file would delete the app.

Unpacking the APK files would just take up more storage and take longer to access when you run the app.