There is no possible way to control the modules on Azure Hybrid workers via Azure Automation. The modules control functionality in Azure Automation is only for the Azure Workers (the built-in ones). This means you will have to do it manually, by running scripts on your machines or some other automation way.

Not that you can write your runbooks in a way that it checks if certain module and version is available on the machine. If it is not available you can have a code that installs the module and the version. That of course will add additional runtime for your runbooks of doing that check and more additional time if it has to download and install the module(s).