Do the shims overlap the ends of the bearing shells, or do the bearings butt together and the shims go only between the block and main bearing cap? If the shims overlap the ends of the bearing, removing a layer of shim will alter the oil clearance, just like on a Babbit rod. If they're only there to make the hole round and the bearing doesn't contact the shim, it would be necessary to also file the end of the bearing a little to alter the oil clearance by removing shims.
Jerry