Like any other Windows program, the normal uninstallers only remove files which were included in their original installer ( because the uninstaller is automatically generate at install time ), which means they normally don't know anything about files that are being added later, during updates ( the uninstaller is not remade adding those ).
That's why, to completely remove a product, you must uninstall the Addon Manager OR reply Yes to the question "Do you want to remove the Addon Manager ?" which is made by every FSX/P3D Uninstall at the end of the normal Uninstall process. This removes the whole Addon Manager folder, so you can start from scratch.
Activation and license have nothing to do with this. You can keep the activation, or not, it's your choice, but it won't affect ( or be affected in any way ) by uninstalling. So you can play with uninstalling/reinstalling as many times as you want and, as long you don't update your hardware or reinstall Windows, you'll never have to worry about reactivation.