Is there an accepted procedure to encrypt the data in a “ConfigurationData.psd1” file? I don’t want to leave IP or hostnames (etc) in config files that are checked in to source code.
There’s nothing native, no. You can certainly encrypt it manually, knowing that you’ll have to manually decrypt it before feeding it to your configuration script.
I could work that in to the flow, thanks 
Alternatively you can check that data into a separate repo with unique permissions. This is relatively common.