ConfigMgr includes an SMS_Processor class as part of hardware inventory that contains an attribute called "Is Hyperthreaded Enabled"; this property if disabled by default but you can enable it. There are no built-in reports showing the data but you can either write your own or use an in-console query to show the data.
You could also use a script (or CMPivot even) to query the Win32_Processor WMI class and compare the value of the NumberOfLogicalProcessors and NumberOfCores attributes. Here's a sample script: http://jeffwouters.nl/index.php/2016/10/powershell-is-hyperthreading-enabled/