If you get this message when you are running validate.php as a non-librenms user and not when you run it as librenms. That means the dependencies are installed into the librenms user’s home directory. When you run python as another user, it cannot access those dependencies.
Only the librenms user needs access to the dependencies. python is NEVER run in the webserver or as root. If validate.php as librenms is good, you are good.
Now that you know everything is ok. If you want to get the warning to go away, simply install the dependencies into the system as root, that way all users have access to them. Many systems do not have new enough python packages in their repository so this likely means using pip3 to install them. (at the time of this writing at least Debian 10 and Ubuntu 20.04 can use apt packages)