pk&flatpak: Drop code paths appending .desktop file at the end of some ids

It ultimately makes everything a bit slower and a lot of the problems that this tried to solve have largely been addressed in different alternative ways or just got fixed downstream.

Test plan: It's especially important making sure that duplicates still get properly detected and that opening with Discover with a URL (e.g. from the web browser, KRunner or $ plasma-discover appstream://org.kde.kate.desktop) still work.