I know Dude has one option to mass upgrade RouterOS version, but this upgrade it's done uploading the npk files from the Dude Box to each RouterOS device.

Why not add one option to use remotely the auto-upgrade option RouterOS has? This it's done in System/Packages/Check for Updates or in the Quick Set window with a button with the same name.

Using this option each selected RouterOs will download it's NPK from the Mikrotik servers instead of uploading the previously downloaded files from the Dude to each routerOS device.