The update manager is designed such that it can install updates without needing administrative/root privileges (which dpkg requires).
Duplicati’s “install” is just an unpacking of the archive (zip in most cases). The deb file is installed in /lib IIRC, and you can uninstall that via the package manager. The updates are stored in ~/.config/duplicati/Updates (you can get the exact info by running mono Duplicati.Library.AutoUpdater.exe info).
The package manager does not know anything about the updates you have installed, so it will leave them behind if you uninstall. But you can simply remove the folder and the update will be uninstalled.