On a 2009 Road King Classic, when ridden over bumps and or holes in the street, it makes a metal to metal, bottoming out sound.

I verified that the stock shocks have air yet it still makes this noise.

Short of bringing it in to Harley, from actual experience, what could be the cause?

 

It might not be the shocks. Check out your exhaust brackets. On mine, the bracket under the bike that held the crossover pipe was not snug on the pipe, so on a significant bump it produced a "clank" that I thought was the rear shocks. I put a shim in there and no more clank.

 

I'd check the swingarm bushings too