Does deleting Mac App Store apps in Launchpad delete related files in the Library folders too?
I tried uninstalling some applications, and files in these folders or the corresponding folders in ~/Library/Containers/ were sometimes deleted and sometimes not:


~/Library/Caches/ (deleted for most applications)
~/Library/Application Support/


Files in these folders weren't deleted for any of the applications I tested with:


~/Library/Preferences/
~/Library/Saved Application State/
/var/db/receipts/
~/Library/Logs/DiagnosticReports/
~/Library/Application Support/CrashReporter/
~/Library/Caches/com.plausiblelabs.crashreporter.data/
~/Library/Application Support/Growl/Tickets/


For example Kindle books or the database for notes in JustNotes were not deleted.

You can see what files are accessed by uninstalld with sudo opensnoop -n uninstalld and search for support files with mdfind $(osascript -e 'id of app "AppName"'). If you want to uninstall applications more completely, it's probably safe to just delete the whole sandbox containers in ~/Library/Containers/.