Does Intune support any ways of deleting of stale device objects or otherwise the bulk deleting computer objects from Intune? I know from the AzureAD preview module you can use remove-azureADdevice, but does this cleanly remove the device in Intune as well? Is there a better way to manage devices en masse?
nothing built in so you need to take care of your own. You can run PowerShell scripts against AzureAD and Intune. For AzureAD you have the AzureAD module and for Intune you can use the Intune API via Microsoft Graph. Some example scripts are here: https://github.com/microsoftgraph/powershell-intune-samples