I solved this issue by generating list of non standard (by standard Hardware ID I mean USB\ROOT_HUB and USB\ROOT_HUB20) Hardware IDs in user-space application and storing it in registry. I enumerate all GUID_DEVINTERFACE_USB_HOST_CONTROLLER instances and assume that children are Root Hubs.
Driver checks if the Hardware ID is present in registry entry generated by user-space application. If it matches, it is considered a Root Hub.