I just purchased a Really Right Stuff L-bracket for my Nikon D7000. Both the RRS bracket (BD7000-L set) and the Kirk bracket that is specifically made for the D7000 (BL-D7000) have a slot in the bracket where it is mounted on the bottom of the camera body. This slot allows the bracket to be slid over to accommodate connections to the various functions on the side of the camera (USB Connector, external mic, etc.).
You can't really open the connector covers without sliding the bracket over in the slot for these brackets.