Is there any module which could help to manage policykit rules on puppet for Ubuntu 16.04 instead of putting file on /etc/polkit-1/localauthority/50-local.d ?
It appears that there is. For future reference, the best place to look for puppet modules generally is to search Puppet Forge. That is the central repository for modules and any module uploaded there can be installed using puppet by typing:
puppet module install jhoblitt-policykit
But obviously, you will want to update the name of the module to be whatever you want to install.