You can identify which host controllers are connected to devices by changing the Device Manager to "View devices by connection" in its View menu.
"Tell me if my device can perform faster" should only affect devices that are USB hi-speed capable, but connected to a port (perhaps through a USB 1.x hub) that is only USB Full speed. Note that USB 2.0 requires that a compliant hub be hi-speed capable.
If you are seeing those warnings regularly, then you have hi-speed devices that are connected in a way that limits their bandwidth. Enabling or disabling the USB Host devices will have no effect on that issue, except that disabling a host that is connected to such a device will both stop the warning and prevent the device from being used.
As others have said, it is quite common to use USB as the on-board interconnect even for the keyboard and track-pad that would classically have been connected via an internal PS2 port or something similar. You'll also see the audio devices on the internal USB occasionally.