we do not have a commandlet that deletes files from Vault, but you can use the Vault API to achieve that.
There are a couple of functions in the DocumentService that might be what you need.
You can find a detailed description of all of them in the Vault SDK help file in Autodesk.Connectivity.WebServices Namespace : DocumentService Class
In powershell this could look something like this for the DeleteFileFromFolder function
$folder = $vault.DocumentService.GetFolderByPath($file._EntityPath)
$vault.DocumentService.DeleteFileFromFolder($file.MasterId, $folder.Id )