Squeaking is the result of 2 surfaces 'rubbing under compression/force'. As wood expands and contracts, and as nails are worked loose, they begin to squeak. In this example, it's the nail riding 'up and down' in the subfloor that's squeaking. Yes, 2 pieces of wood can squeak but in your case, I don't think the beams are your problem.
If you look at your Contractors 'solution', he's trying to prevent the subfloor from moving up and down by hammering in the shims. If he's successful, then you'd have no more squeaking. Again, I don't think the beams are your problem. Did he nail or screw the subfloor down? If it's nailed, that would explain the squeaking. If it's screwed down, then I don't know what it is. Maybe there's ductwork under there that's 'moving' when you walk on the floor?
There are alternatives to shims. Look at Squeak Relief I and Squeak-Relief II. It's the same product. The key to this is access to the subfloor from underneath. (I think you do because you said your Contractor is hammering in shims.) And lastly, start poking around for other alternatives at Google.com Squeaky Floors.