Windows does not install drivers for non-existant hardware.
In addition to the USB ports being "hidden"
(if this is an AT style motherboard, the USB ports are on an internal header)
(if an ATX, the ports may be blocked by a removeable panel on the I/O sheild)
It is possible that the driver was installed by the Chipset / motherboard driver utility.
The simplest thing to check, is to enter setup at boot, and look in the onboard periphials section.
If USB ports are listed, and enabled,they are there.
If you want to remove them, first remove them from device manager, then shutdown, and enter setup when you re-boot and disable the ports.
If you wish to use them, you will need to check the motherboard manual for the proper pinout and location of the header.
Then, get either a card slot adapter cable, or a front panel (drive bay) adapter.
Chas