Sorry I couldn't be of more assistance, but I do have some questions.
1. I'm assuming this is a used car purchase?
2. If so, how many miles on the odometer?
3. If the USB cable is completely missing from the console, it begs the question was this car involved in an accident and the USB port was left out in the repair.
4. This might explain the dealer's reluctance to talk about it. I'm thinking it was an auction car that they put on their lot to sell.
5. Might be worth paying for a CarFax report to see it's history.
My son bought a used Civic coupe from a Honda dealer once and after a few months rust developed in the driver's side rear quarter panel. When we took the interior apart to check to see if the rust was elsewhere, we found broken glass inside the body from the rear quarter window. Obviously, the car had been in an accident earlier in it's life. The dealer may/may not have known about it.
Oh yeah, the USB cable may plug into the wiring harness of the dash and not into the audio unit itself. In my car, the iMID and the Nav unit display slightly different song information when playing USB drives. The iMID shows the song title from the title field and the Nav shows the song title from file name. It doesn't explain how they are connected, but it suggests they are sharing the input from the USB port.